galaxy-dev November 2009

galaxy-dev@lists.galaxyproject.org

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233 discussions

[hg] galaxy 2957: AMQP messaging server and client files.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5b2d593d9aed changeset: 2957:5b2d593d9aed user: rc date: Wed Nov 04 10:04:51 2009 -0500 description: AMQP messaging server and client files. diffstat: scripts/galaxy_messaging/amqp_consumer.py | 94 ------------- scripts/galaxy_messaging/client/amqp_publisher.py | 87 ++++++++++++ scripts/galaxy_messaging/client/galaxy_amq.ini.sample | 32 ++++ scripts/galaxy_messaging/client/report.bat.sample | 1 + scripts/galaxy_messaging/client/scan.bat.sample | 1 + scripts/galaxy_messaging/client/scan.sh.sample | 1 + scripts/galaxy_messaging/client/scanner.py | 92 +++++++++++++ scripts/galaxy_messaging/client/scanner_interface.py | 76 ++++++++++ scripts/galaxy_messaging/galaxydb_interface.py | 151 --------------------- scripts/galaxy_messaging/server/amqp_consumer.py | 94 +++++++++++++ scripts/galaxy_messaging/server/galaxydb_interface.py | 149 +++++++++++++++++++++ 11 files changed, 533 insertions(+), 245 deletions(-) diffs (829 lines): diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/amqp_consumer.py --- a/scripts/galaxy_messaging/amqp_consumer.py Wed Nov 04 09:32:09 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -''' -Galaxy Messaging with AMQP (RabbitMQ) -Galaxy uses AMQ protocol to receive messages from external sources like -bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -For Galaxy to receive messages from a message queue the RabbitMQ server has -to be set up with a user account and other parameters listed in the [galaxy:amq] -section in the universe_wsgi.ini config file -Once the RabbitMQ server has been setup and started with the given parameters, -this script can be run to receive messages and update the Galaxy database accordingly -''' - -import ConfigParser -import sys, os -import optparse -import xml.dom.minidom -from galaxydb_interface import GalaxyDbInterface - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -import pkg_resources -pkg_resources.require( "amqplib" ) - -from amqplib import client_0_8 as amqp - -import logging -logging.basicConfig(level=logging.DEBUG) -log = logging.getLogger( 'GalaxyAMQP' ) - - -galaxy_config_file = 'universe_wsgi.ini' -global dbconnstr - -def get_value(dom, tag_name): - ''' - This method extracts the tag value from the xml message - ''' - nodelist = dom.getElementsByTagName(tag_name)[0].childNodes - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - -def recv_callback(msg): - dom = xml.dom.minidom.parseString(msg.body) - barcode = get_value(dom, 'barcode') - state = get_value(dom, 'state') - log.debug('Barcode: '+barcode) - log.debug('State: '+state) - # update the galaxy db - galaxy = GalaxyDbInterface(dbconnstr) - sample_id = galaxy.get_sample_id(field_name='bar_code', value=barcode) - if sample_id == -1: - log.debug('Invalid barcode.') - return - galaxy.change_state(sample_id, state) - -def main(): - config = ConfigParser.ConfigParser() - config.read(galaxy_config_file) - global dbconnstr - dbconnstr = config.get("app:main", "database_connection") - amqp_config = {} - for option in config.options("galaxy:amqp"): - amqp_config[option] = config.get("galaxy:amqp", option) - log.debug(str(amqp_config)) - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'], - insist=False) - chan = conn.channel() - chan.queue_declare(queue=amqp_config['queue'], durable=True, exclusive=True, auto_delete=False) - chan.exchange_declare(exchange=amqp_config['exchange'], type="direct", durable=True, auto_delete=False,) - chan.queue_bind(queue=amqp_config['queue'], - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) - - chan.basic_consume(queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, - consumer_tag="testtag") - while True: - chan.wait() - chan.basic_cancel("testtag") - chan.close() - conn.close() - -if __name__ == '__main__': - main() \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/amqp_publisher.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/amqp_publisher.py Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,87 @@ +''' +This script gets barcode data from a barcode scanner using serial communication +and sends the state representated by the barcode scanner & the barcode string +to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, +barcode & state. The state of the scanner should be set in the galaxy_amq.ini +file as a configuration variable. +''' + +from amqplib import client_0_8 as amqp +import ConfigParser +import sys, os +import serial +import array +import time +import optparse + + +xml = \ +''' <sample> + <barcode>%(BARCODE)s</barcode> + <state>%(STATE)s</state> + </sample>''' + + +def handle_scan(states, amqp_config, barcode): + if states.get(barcode[:2], None): + values = dict( BARCODE=barcode[2:], + STATE=states.get(barcode[:2]) ) + print values + data = xml % values + print data + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host'], + insist=False) + chan = conn.channel() + msg = amqp.Message(data) + msg.properties["delivery_mode"] = 2 + chan.basic_publish(msg, + exchange=amqp_config['exchange'], + routing_key=amqp_config['routing_key']) + chan.close() + conn.close() + +def recv_data(states, amqp_config, s): + while True: + bytes = s.inWaiting() + if bytes: + print '%i bytes recvd' % bytes + msg = s.read(bytes) + print msg + handle_scan(states, amqp_config, msg.strip()) + + +def main(): + parser = optparse.OptionParser() + parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', + dest='config_file', action='store') + parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', + dest='port', action='store') + (opts, args) = parser.parse_args() + config = ConfigParser.ConfigParser() + config.read(opts.config_file) + amqp_config = {} + states = {} + for option in config.options("galaxy:amqp"): + amqp_config[option] = config.get("galaxy:amqp", option) + count = 1 + while True: + section = 'scanner%i' % count + if config.has_section(section): + states[config.get(section, 'prefix')] = config.get(section, 'state') + count = count + 1 + else: + break + print amqp_config + print states + s = serial.Serial(int(opts.port)) + print 'Port %s is open: %s' %( opts.port, s.isOpen()) + recv_data(states, amqp_config, s) + s.close() + print 'Port %s is open: %s' %( opts.port, s.isOpen()) + + +if __name__ == '__main__': + main() diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/galaxy_amq.ini.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/galaxy_amq.ini.sample Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,32 @@ +# Galaxy Message Queue +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +#[galaxy:amqp] +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner + +# The following section(s) 'scanner#' is for specifying the state of the +# sample this scanner represents. This state name should be one of the +# possible states created for this request type in Galaxy +# If there multiple scanners attached to this host the add as many "scanner#" +# sections below each with the name & prefix of the bar code scanner and +# the state it represents +#[scanner1] +#name = +#state = +#prefix = + +#[scanner2] +#name = +#state = +#prefix = \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/report.bat.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/report.bat.sample Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,1 @@ +python scanner.py -p 2 -c galaxy_amq.ini -r \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/scan.bat.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/scan.bat.sample Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,1 @@ +python amqp_publisher.py -p 2 -c galaxy_amq.ini \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/scan.sh.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/scan.sh.sample Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,1 @@ +python amqp_publisher.py -p 3 -c galaxy_amq.ini \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/scanner.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/scanner.py Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,92 @@ +import sys, os +import serial +import array +import time +import optparse +import ConfigParser, logging +from scanner_interface import ScannerInterface + +logging.basicConfig(level=logging.DEBUG) +log = logging.getLogger( 'Scanner' ) + +# command prefix: SYN M CR +cmd = [22, 77, 13] +response = { 6: 'ACK', 5: 'ENQ', 21: 'NAK' } +image_scanner_report = 'RPTSCN.' +get_prefix1 = 'PREBK2?.' +get_prefix2 = ':4820:PREBK2?.' +set_prefix = 'PREBK2995859.' +clear_prefix = 'PRECA2.' + +def get_prefix_cmd(name): + return ':' + name + ':' + 'PREBK2?.' + +def set_prefix_cmd(name, prefix): + prefix_str = '' + for c in prefix: + prefix_str = prefix_str + hex(ord(c))[2:] + return ':' + name + ':' + 'PREBK299' + prefix_str + '!' + +def read_config_file(config_file): + config = ConfigParser.ConfigParser() + config.read(config_file) + count = 1 + scanners_list = [] + while True: + section = 'scanner%i' % count + if config.has_section(section): + scanner = dict(name=config.get(section, 'name'), + prefix=config.get(section, 'prefix'), + state=config.get(section, 'state')) + scanners_list.append(scanner) + count = count + 1 + else: + return scanners_list + +def main(): + usage = "python %s -p PORT -c CONFIG_FILE [ OPTION ]" % sys.argv[0] + parser = optparse.OptionParser(usage=usage) + parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', + dest='port', action='store') + parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', + dest='config_file', action='store') + parser.add_option('-r', '--report', help='scanner report', + dest='report', action='store_true', default=False) + parser.add_option('-i', '--install', help='install the scanners', + dest='install', action='store_true', default=False) + (opts, args) = parser.parse_args() + # validate + if not opts.port: + parser.print_help() + sys.exit(0) + if ( opts.report or opts.install ) and not opts.config_file: + parser.print_help() + sys.exit(0) + + # create the scanner interface + si = ScannerInterface(opts.port) + if opts.install: + scanners_list = read_config_file(opts.config_file) + for scanner in scanners_list: + msg = set_prefix_cmd(scanner['name'], scanner['prefix']) + si.send(msg) + response = si.recv() + if not response: + log.error("Scanner %s could not be installed." % scanner['name']) + elif opts.report: + si.send(image_scanner_report) + rep = si.recv() + log.info(rep) + scanners_list = read_config_file(opts.config_file) + for scanner in scanners_list: + msg = get_prefix_cmd(scanner['name']) + si.send(msg) + response = si.recv() + if response: + log.info('PREFIX for scanner %s: %s' % (scanner['name'], chr(int(response[8:12][:2], 16))+chr(int(response[8:12][2:], 16)) )) + si.close() + + + +if __name__ == "__main__": + main() diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/client/scanner_interface.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/client/scanner_interface.py Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,76 @@ +import sys, os +import serial +import array +import time +import optparse +import ConfigParser +import logging + +logging.basicConfig(level=logging.INFO) +log = logging.getLogger( 'ScannerInterface' ) + +class ScannerInterface( object ): + cmdprefix = [22, 77, 13] + response = { 6: 'ACK', 5: 'ENQ', 21: 'NAK' } + + def __init__( self, port ): + if os.name in ['posix', 'mac']: + self.port = port + elif os.name == 'nt': + self.port = int(port) + if self.port: + self.open() + + def open(self): + try: + self.serial_conn = serial.Serial(self.port) + except serial.SerialException: + log.exception('Unable to open port: %s' % str(self.port)) + sys.exit(1) + log.debug('Port %s is open: %s' %( str(self.port), self.serial_conn.isOpen() ) ) + + def is_open(self): + return self.serial_conn.isOpen() + + def close(self): + self.serial_conn.close() + log.debug('Port %s is open: %s' %( str(self.port), self.serial_conn.isOpen() ) ) + + def send(self, msg): + message = self.cmdprefix + map(ord, msg) + byte_array = array.array('B', message) + log.debug('Sending message to %s: %s' % ( str(self.port), message) ) + bytes = self.serial_conn.write( byte_array.tostring() ) + log.debug('%i bytes out of %i bytes sent to the scanner' % ( bytes, len(message) ) ) + + def recv(self): + time.sleep(1) + self.serial_conn.flush() + nbytes = self.serial_conn.inWaiting() + log.debug('%i bytes received' % nbytes) + if nbytes: + msg = self.serial_conn.read(nbytes) + byte_array = map(ord, msg) + log.debug('Message received [%s]: %s' % (self.response.get(byte_array[len(byte_array)-2], byte_array[len(byte_array)-2]), + msg)) + return msg + else: + log.error('Error!') + return None + + def setup_recv(self, callback): + self.recv_callback = callback + + def wait(self): + nbytes = self.serial_conn.inWaiting() + if nbytes: + msg = self.serial_conn.read(nbytes) + byte_array = map(ord, msg) + log.debug('Message received [%s]: %s' % (self.response.get(byte_array[len(byte_array)-2], byte_array[len(byte_array)-2], + msg))) + if self.recv_callback: + self.recv_callback(msg) + return + + + \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/galaxydb_interface.py --- a/scripts/galaxy_messaging/galaxydb_interface.py Wed Nov 04 09:32:09 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,151 +0,0 @@ -#/usr/bin/python - -from datetime import datetime, timedelta -import sys -import optparse -import os -import time -import logging - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path -from galaxy import eggs -import pkg_resources -pkg_resources.require( "psycopg2" ) -import psycopg2 -pkg_resources.require( "SQLAlchemy >= 0.4" ) -from sqlalchemy import * -from sqlalchemy.orm import sessionmaker - -logging.basicConfig(level=logging.DEBUG) -log = logging.getLogger( 'GalaxyDbInterface' ) - -class GalaxyDbInterface(object): - - def __init__(self, dbstr): - self.dbstr = dbstr - self.db_engine = create_engine(self.dbstr) -# self.db_engine.echo = True - self.metadata = MetaData(self.db_engine) - self.session = sessionmaker(bind=self.db_engine) - self.event_table = Table('sample_event', self.metadata, autoload=True ) - self.sample_table = Table('sample', self.metadata, autoload=True ) - self.request_table = Table('request', self.metadata, autoload=True ) - self.state_table = Table('sample_state', self.metadata, autoload=True ) - - def get_sample_id(self, field_name='bar_code', value=None): - if not value: - return -1 - sample_id = -1 - if field_name =='name': - stmt = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.name==value) - result = stmt.execute() - sample_id = result.fetchone()[0] - elif field_name == 'bar_code': - stmt = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.bar_code==value) - result = stmt.execute() - x = result.fetchone() - if x: - sample_id = x[0] - log.debug('Sample ID: %i' % sample_id) - return sample_id - log.warning('This sample %s %s does not belong to any sample in the database.' % (field_name, value)) - return -1 - - def current_state(self, sample_id): - ''' - This method returns the current state of the sample for the given sample_id - ''' - stmt = select(columns=[self.event_table.c.sample_state_id], - whereclause=self.event_table.c.sample_id==sample_id, - order_by=self.event_table.c.update_time.desc()) - result = stmt.execute() - all_states = result.fetchall() - current_state_id = all_states[0][0] - return current_state_id - - def all_possible_states(self, sample_id): - subsubquery = select(columns=[self.sample_table.c.request_id], - whereclause=self.sample_table.c.id==sample_id) - self.request_id = subsubquery.execute().fetchall()[0][0] - log.debug('REQUESTID: %i' % self.request_id) - subquery = select(columns=[self.request_table.c.request_type_id], - whereclause=self.request_table.c.id==self.request_id) - request_type_id = subquery.execute().fetchall()[0][0] - log.debug('REQUESTTYPEID: %i' % request_type_id) - query = select(columns=[self.state_table.c.id, self.state_table.c.name], - whereclause=self.state_table.c.request_type_id==request_type_id, - order_by=self.state_table.c.id.asc()) - states = query.execute().fetchall() - log.debug('POSSIBLESTATES: '+ str(states)) - return states - - def change_state(self, sample_id, new_state=None): - ''' - This method changes the state of the sample to the the 'new_state' - ''' - if not new_state: - return - new_state_id = -1 - # find the state_id for this new state in the list of possible states - possible_states = self.all_possible_states(sample_id) - for state_id, state_name in possible_states: - if new_state == state_name: - new_state_id = state_id - if new_state_id == -1: - return - log.debug('Updating sample_id %i state to %s' % (sample_id, new_state)) - d = timedelta(hours=4) - i = self.event_table.insert() - i.execute(update_time=datetime.now()+d, - create_time=datetime.now()+d, - sample_id=sample_id, - sample_state_id=int(new_state_id), - comment='bar code scanner') - # if all the samples for this request are in the final state - # then change the request state to 'Complete' - result = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.request_id==self.request_id).execute() - sample_id_list = result.fetchall() - request_complete = True - for sid in sample_id_list: - current_state_id = self.current_state(sid[0]) - if current_state_id != possible_states[-1][0]: - request_complete = False - break - if request_complete: - request_state = 'Complete' - else: - request_state = 'Submitted' - log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state)) - d = timedelta(hours=4) - i = self.request_table.update(whereclause=self.request_table.c.id==self.request_id, - values={self.request_table.c.state: request_state}) - i.execute() - - - -if __name__ == '__main__': - print '''This file should not be run directly. To start the Galaxy AMQP Listener: - %sh run_galaxy_listener.sh''' -# dbstr = 'postgres://postgres:postgres@localhost/galaxy_ft' -# -# parser = optparse.OptionParser() -# parser.add_option('-n', '--name', help='name of the sample field', dest='name', \ -# action='store', default='bar_code') -# parser.add_option('-v', '--value', help='value of the sample field', dest='value', \ -# action='store') -# parser.add_option('-s', '--state', help='new state of the sample', dest='state', \ -# action='store') -# (opts, args) = parser.parse_args() -# -# gs = GalaxyDbInterface(dbstr) -# sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value) -# gs.change_state(sample_id, opts.state) - - - diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/server/amqp_consumer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/server/amqp_consumer.py Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,94 @@ +''' +Galaxy Messaging with AMQP (RabbitMQ) +Galaxy uses AMQ protocol to receive messages from external sources like +bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +For Galaxy to receive messages from a message queue the RabbitMQ server has +to be set up with a user account and other parameters listed in the [galaxy:amq] +section in the universe_wsgi.ini config file +Once the RabbitMQ server has been setup and started with the given parameters, +this script can be run to receive messages and update the Galaxy database accordingly +''' + +import ConfigParser +import sys, os +import optparse +import xml.dom.minidom +from galaxydb_interface import GalaxyDbInterface + +assert sys.version_info[:2] >= ( 2, 4 ) +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "amqplib" ) + +from amqplib import client_0_8 as amqp + +import logging +logging.basicConfig(level=logging.DEBUG) +log = logging.getLogger( 'GalaxyAMQP' ) + + +galaxy_config_file = 'universe_wsgi.ini' +global dbconnstr + +def get_value(dom, tag_name): + ''' + This method extracts the tag value from the xml message + ''' + nodelist = dom.getElementsByTagName(tag_name)[0].childNodes + rc = "" + for node in nodelist: + if node.nodeType == node.TEXT_NODE: + rc = rc + node.data + return rc + +def recv_callback(msg): + dom = xml.dom.minidom.parseString(msg.body) + barcode = get_value(dom, 'barcode') + state = get_value(dom, 'state') + log.debug('Barcode: '+barcode) + log.debug('State: '+state) + # update the galaxy db + galaxy = GalaxyDbInterface(dbconnstr) + sample_id = galaxy.get_sample_id(field_name='bar_code', value=barcode) + if sample_id == -1: + log.debug('Invalid barcode.') + return + galaxy.change_state(sample_id, state) + +def main(): + config = ConfigParser.ConfigParser() + config.read(galaxy_config_file) + global dbconnstr + dbconnstr = config.get("app:main", "database_connection") + amqp_config = {} + for option in config.options("galaxy:amqp"): + amqp_config[option] = config.get("galaxy:amqp", option) + log.debug(str(amqp_config)) + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host'], + insist=False) + chan = conn.channel() + chan.queue_declare(queue=amqp_config['queue'], durable=True, exclusive=True, auto_delete=False) + chan.exchange_declare(exchange=amqp_config['exchange'], type="direct", durable=True, auto_delete=False,) + chan.queue_bind(queue=amqp_config['queue'], + exchange=amqp_config['exchange'], + routing_key=amqp_config['routing_key']) + + chan.basic_consume(queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, + consumer_tag="testtag") + while True: + chan.wait() + chan.basic_cancel("testtag") + chan.close() + conn.close() + +if __name__ == '__main__': + main() \ No newline at end of file diff -r 984b1eb6c428 -r 5b2d593d9aed scripts/galaxy_messaging/server/galaxydb_interface.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/server/galaxydb_interface.py Wed Nov 04 10:04:51 2009 -0500 @@ -0,0 +1,149 @@ +#/usr/bin/python + +from datetime import datetime +import sys +import optparse +import os +import time +import logging + +assert sys.version_info[:2] >= ( 2, 4 ) +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path +from galaxy import eggs +import pkg_resources +pkg_resources.require( "psycopg2" ) +import psycopg2 +pkg_resources.require( "SQLAlchemy >= 0.4" ) +from sqlalchemy import * +from sqlalchemy.orm import sessionmaker + +logging.basicConfig(level=logging.DEBUG) +log = logging.getLogger( 'GalaxyDbInterface' ) + +class GalaxyDbInterface(object): + + def __init__(self, dbstr): + self.dbstr = dbstr + self.db_engine = create_engine(self.dbstr) +# self.db_engine.echo = True + self.metadata = MetaData(self.db_engine) + self.session = sessionmaker(bind=self.db_engine) + self.event_table = Table('sample_event', self.metadata, autoload=True ) + self.sample_table = Table('sample', self.metadata, autoload=True ) + self.request_table = Table('request', self.metadata, autoload=True ) + self.state_table = Table('sample_state', self.metadata, autoload=True ) + + def get_sample_id(self, field_name='bar_code', value=None): + if not value: + return -1 + sample_id = -1 + if field_name =='name': + stmt = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.name==value) + result = stmt.execute() + sample_id = result.fetchone()[0] + elif field_name == 'bar_code': + stmt = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.bar_code==value) + result = stmt.execute() + x = result.fetchone() + if x: + sample_id = x[0] + log.debug('Sample ID: %i' % sample_id) + return sample_id + log.warning('This sample %s %s does not belong to any sample in the database.' % (field_name, value)) + return -1 + + def current_state(self, sample_id): + ''' + This method returns the current state of the sample for the given sample_id + ''' + stmt = select(columns=[self.event_table.c.sample_state_id], + whereclause=self.event_table.c.sample_id==sample_id, + order_by=self.event_table.c.update_time.desc()) + result = stmt.execute() + all_states = result.fetchall() + current_state_id = all_states[0][0] + return current_state_id + + def all_possible_states(self, sample_id): + subsubquery = select(columns=[self.sample_table.c.request_id], + whereclause=self.sample_table.c.id==sample_id) + self.request_id = subsubquery.execute().fetchall()[0][0] + log.debug('REQUESTID: %i' % self.request_id) + subquery = select(columns=[self.request_table.c.request_type_id], + whereclause=self.request_table.c.id==self.request_id) + request_type_id = subquery.execute().fetchall()[0][0] + log.debug('REQUESTTYPEID: %i' % request_type_id) + query = select(columns=[self.state_table.c.id, self.state_table.c.name], + whereclause=self.state_table.c.request_type_id==request_type_id, + order_by=self.state_table.c.id.asc()) + states = query.execute().fetchall() + log.debug('POSSIBLESTATES: '+ str(states)) + return states + + def change_state(self, sample_id, new_state=None): + ''' + This method changes the state of the sample to the the 'new_state' + ''' + if not new_state: + return + new_state_id = -1 + # find the state_id for this new state in the list of possible states + possible_states = self.all_possible_states(sample_id) + for state_id, state_name in possible_states: + if new_state == state_name: + new_state_id = state_id + if new_state_id == -1: + return + log.debug('Updating sample_id %i state to %s' % (sample_id, new_state)) + i = self.event_table.insert() + i.execute(update_time=datetime.utcnow(), + create_time=datetime.utcnow(), + sample_id=sample_id, + sample_state_id=int(new_state_id), + comment='bar code scanner') + # if all the samples for this request are in the final state + # then change the request state to 'Complete' + result = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.request_id==self.request_id).execute() + sample_id_list = result.fetchall() + request_complete = True + for sid in sample_id_list: + current_state_id = self.current_state(sid[0]) + if current_state_id != possible_states[-1][0]: + request_complete = False + break + if request_complete: + request_state = 'Complete' + else: + request_state = 'Submitted' + log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state)) + i = self.request_table.update(whereclause=self.request_table.c.id==self.request_id, + values={self.request_table.c.state: request_state}) + i.execute() + + + +if __name__ == '__main__': + print '''This file should not be run directly. To start the Galaxy AMQP Listener: + %sh run_galaxy_listener.sh''' + dbstr = 'postgres://postgres:postgres@localhost/galaxy_uft' + + parser = optparse.OptionParser() + parser.add_option('-n', '--name', help='name of the sample field', dest='name', \ + action='store', default='bar_code') + parser.add_option('-v', '--value', help='value of the sample field', dest='value', \ + action='store') + parser.add_option('-s', '--state', help='new state of the sample', dest='state', \ + action='store') + (opts, args) = parser.parse_args() + + gs = GalaxyDbInterface(dbstr) + sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value) + gs.change_state(sample_id, opts.state) + + +

1 0

[hg] galaxy 2948: Pack recently modified scripts.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/de764999c5af changeset: 2948:de764999c5af user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 13:00:36 2009 -0500 description: Pack recently modified scripts. diffstat: static/scripts/packed/autocomplete_tagging.js | 2 +- static/scripts/packed/trackster.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (16 lines): diff -r f776fa6045ba -r de764999c5af static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 12:58:13 2009 -0500 +++ b/static/scripts/packed/autocomplete_tagging.js Tue Nov 03 13:00:36 2009 -0500 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u,v){},editable:true,input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};v ar s=b();if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E .after(D)}else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){tag_name_and_value=u.split(":");p.tag_click_fn(tag_name_and_value[0],tag_name_and_value[1]);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);if(p.editable){x.append(v)}return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true) {return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,fo rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file +var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" 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rmatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});if(p.editable){m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false})}if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file diff -r f776fa6045ba -r de764999c5af static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Tue Nov 03 12:58:13 2009 -0500 +++ b/static/scripts/packed/trackster.js Tue Nov 03 13:00:36 2009 -0500 @@ -1,1 +1,1 @@ -var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=5,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(l eft_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e =this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){thi s.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k)}if(g){this.tile_cache.set(i,g)}a+=1}}});var LabelTrack=function(a){Track.ca ll(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dat aset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[e]=g;$(document).trigger("redra w")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(FeatureTrack.prototype,TiledTrack.pro totype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.container_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k=Math.floor(Math.max(e,(n.star t-e)*g));k-=m.measureText(n.name).width;l=Math.ceil(Math.min(a,(n.end-e)*g))}else{k=Math.floor(Math.max(e,(n.start-e)*b));l=Math.ceil(Math.min(a,(n.end-e)*b))}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospac e";v.textAlign="right";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}els e{if(f.strand=="-"){v.fillStyle=LEFT_STRAND_INV}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}}}y++}}g.append(s);return s}}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES=10,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern( left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){ e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){th is.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.tile_cache=new Cache(CACHED_TILES)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var h=this.view.low,d=this.view.high,e=d-h;var c=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));c=Math.max(c,0.1);c=Math.min(c,1000000);var j=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(j);var k=this.content_div.width()/e;var g;var a=Math.floor(h/c/DENSITY);while((a*DENSITY*c)<d){var i=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var b=this.tile_cache.get(i);if(b){var f=a*DENSITY*c;b.css({left:(f-this.view.low)*k});j.append(b)}else{g=this.draw_tile(c,a,j,k);if(g){this.tile_cache.set(i,g)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low: null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_px+32+"px",});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id},function(g){c.cache[ e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(Featur eTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},calc_slots:function(o){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),g=this.show_labels_scale,a=this.view.max_high,e=this.view.max_low;if(o){this.zi_slots={}}var m=$("<canvas></canvas>").get(0).getContext("2d");for(var f=0,h=this.values.length;f<h;f++){var k,l,n=this.values[f];if(o){k= Math.floor((n.start-e)*g);k-=m.measureText(n.name).width;l=Math.ceil((n.end-e)*g)}else{k=Math.floor((n.start-e)*b);l=Math.ceil((n.end-e)*b)}var d=0;while(true){if(c[d]===undefined||c[d]<k){c[d]=l;if(o){this.zi_slots[n.name]=d}else{this.zo_slots[n.name]=d}break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},draw_tile:function(w,B,g,n){if(!this.values){return null}if(n>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(n<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var C=B*DENSITY*w,c=(B+1)*DENSITY*w,q=DENSITY*w;var u=Math.ceil(q*n),t=this.height_px,s=$("<canvas class='tile'></canvas>");s.css({position:"absolute",top:0,left:(C-this.view.low)*n});s.get(0).width=u;s.get(0).height=t;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font="10px monospace";v.textAlign="rig ht";var y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}else{if(f.strand=="-") 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1 0

[hg] galaxy 2949: imported patch alchemy05_fixes_01
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/133252175425 changeset: 2949:133252175425 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 12:52:00 2009 -0500 description: imported patch alchemy05_fixes_01 diffstat: eggs.ini | 10 +- lib/galaxy/model/mapping.py | 2 +- lib/galaxy/model/migrate/check.py | 2 +- lib/galaxy/model/migrate/versions/0003_security_and_libraries.py | 4 +- lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py | 2 +- lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py | 4 +- lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py | 2 +- lib/galaxy/model/migrate/versions/0008_galaxy_forms.py | 4 +- lib/galaxy/model/migrate/versions/0009_request_table.py | 2 +- lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py | 4 +- lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py | 4 +- lib/galaxy/model/migrate/versions/0012_user_address.py | 4 +- lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py | 2 +- lib/galaxy/model/migrate/versions/0017_library_item_indexes.py | 2 +- lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py | 2 +- lib/galaxy/model/migrate/versions/0019_request_library_folder.py | 4 +- lib/galaxy/model/migrate/versions/0020_library_upload_job.py | 4 +- lib/galaxy/model/orm/ext/assignmapper.py | 38 ++++++--- lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/page.py | 4 +- lib/galaxy/web/controllers/workflow.py | 22 ++-- lib/galaxy/web/framework/helpers/grids.py | 4 +- 23 files changed, 73 insertions(+), 57 deletions(-) diffs (502 lines): diff -r 80915982fdb2 -r 133252175425 eggs.ini --- a/eggs.ini Tue Nov 03 11:28:34 2009 -0500 +++ b/eggs.ini Tue Nov 03 12:52:00 2009 -0500 @@ -28,6 +28,7 @@ [eggs:noplatform] amqplib = 0.6.1 Beaker = 1.4 +decorator = 3.1.2 docutils = 0.4 elementtree = 1.2.6_20050316 lrucache = 0.2 @@ -41,8 +42,8 @@ PasteScript = 1.3.6 Routes = 1.6.3 simplejson = 1.5 -SQLAlchemy = 0.4.7p1 -sqlalchemy_migrate = 0.4.5 +SQLAlchemy = 0.5.6 +sqlalchemy_migrate = 0.5.4 Tempita = 0.1 twill = 0.9 WebError = 0.8a @@ -77,6 +78,7 @@ guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz amqplib = http://py-amqplib.googlecode.com/files/amqplib-0.6.1.tgz Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz +decorator = http://pypi.python.org/packages/source/d/decorator/decorator-3.1.2.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz @@ -90,8 +92,8 @@ PSI = http://pypi.python.org/packages/source/P/PSI/PSI-0.3b1.1.tar.gz Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… -SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.… -sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… +SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.5.6.tar.gz +sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 @@ -18,7 +18,7 @@ from sqlalchemy.ext.associationproxy import association_proxy metadata = MetaData() -context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) +context = Session = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) # For backward compatibility with "context.current" context.current = Session diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/check.py Tue Nov 03 12:52:00 2009 -0500 @@ -7,7 +7,7 @@ from migrate.versioning import repository, schema from sqlalchemy import * -from sqlalchemy.exceptions import NoSuchTableError +from sqlalchemy.exc import NoSuchTableError log = logging.getLogger( __name__ ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0003_security_and_libraries.py --- a/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0003_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -20,7 +20,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) if migrate_engine.name == 'postgres': # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.ht… diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py --- a/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py Tue Nov 03 12:52:00 2009 -0500 @@ -12,7 +12,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) User_table = Table( "galaxy_user", metadata, autoload=True ) HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Tue Nov 03 12:52:00 2009 -0500 @@ -23,7 +23,7 @@ metadata = MetaData( migrate_engine ) -context = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) +context = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) ## classes @@ -662,7 +662,7 @@ log.debug( "Fixing a discrepancy concerning deleted shared history items." ) affected_items = 0 start_time = time.time() - for dataset in context.query( Dataset ).filter( and_( Dataset.c.deleted == True, Dataset.c.purged == False ) ): + for dataset in context.query( Dataset ).filter( and_( Dataset.deleted == True, Dataset.purged == False ) ): for dataset_instance in dataset.history_associations + dataset.library_associations: if not dataset_instance.deleted: dataset.deleted = False diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py --- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Tue Nov 03 12:52:00 2009 -0500 @@ -16,7 +16,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0008_galaxy_forms.py --- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -11,7 +11,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -31,7 +31,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0009_request_table.py --- a/lib/galaxy/model/migrate/versions/0009_request_table.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Tue Nov 03 12:52:00 2009 -0500 @@ -9,7 +9,7 @@ from migrate.changeset import * import sys, logging from galaxy.model.custom_types import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py --- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Tue Nov 03 12:52:00 2009 -0500 @@ -10,7 +10,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -30,7 +30,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py --- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Tue Nov 03 12:52:00 2009 -0500 @@ -5,7 +5,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * @@ -25,7 +25,7 @@ from galaxy.model.custom_types import * metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0012_user_address.py --- a/lib/galaxy/model/migrate/versions/0012_user_address.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0012_user_address.py Tue Nov 03 12:52:00 2009 -0500 @@ -6,7 +6,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -24,7 +24,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py --- a/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -17,7 +17,7 @@ """ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import sys, logging diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0017_library_item_indexes.py --- a/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0017_library_item_indexes.py Tue Nov 03 12:52:00 2009 -0500 @@ -16,7 +16,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) LibraryDataset_table = Table( "library_dataset", metadata, autoload=True ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py --- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Tue Nov 03 12:52:00 2009 -0500 @@ -5,7 +5,7 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * import migrate.changeset diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0019_request_library_folder.py --- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -18,7 +18,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/migrate/versions/0020_library_upload_job.py --- a/lib/galaxy/model/migrate/versions/0020_library_upload_job.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0020_library_upload_job.py Tue Nov 03 12:52:00 2009 -0500 @@ -1,6 +1,6 @@ from sqlalchemy import * from sqlalchemy.orm import * -from sqlalchemy.exceptions import * +from sqlalchemy.exc import * from migrate import * from migrate.changeset import * import datetime @@ -18,7 +18,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "" diff -r 80915982fdb2 -r 133252175425 lib/galaxy/model/orm/ext/assignmapper.py --- a/lib/galaxy/model/orm/ext/assignmapper.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/model/orm/ext/assignmapper.py Tue Nov 03 12:52:00 2009 -0500 @@ -15,22 +15,36 @@ from sqlalchemy import util, exceptions import types -from sqlalchemy.orm import mapper, Query +from sqlalchemy.orm import Query +from sqlalchemy.orm import mapper as sqla_mapper -def _monkeypatch_session_method(name, session, class_, make_list=False): - def do(self, *args, **kwargs): - if make_list: - self = [ self ] - return getattr(session, name)( self, *args, **kwargs ) +def _monkeypatch_session_method( name, session, class_ ): + # TODO: eliminate this method by fixing the session flushes + def do( self, *args, **kwargs ): + if self not in session.deleted: + session.add( self ) + return session.flush() try: do.__name__ = name except: pass - if not hasattr(class_, name): - setattr(class_, name, do) - + if not hasattr( class_, name ): + setattr( class_, name, do ) +def session_mapper( scoped_session, class_, *args, **kwargs ): + def mapper( cls, *arg, **kw ): + validate = kw.pop( 'validate', False ) + if cls.__init__ is object.__init__: + def __init__( self, **kwargs ): + for key, value in kwargs.items(): + if validate: + if not cls_mapper.has_property( key ): + raise TypeError( "Invalid __init__ argument: '%s'" % key ) + setattr( self, key, value ) + cls.__init__ = __init__ + cls.query = scoped_session.query_property() + _monkeypatch_session_method( 'flush', scoped_session, cls ) + return sqla_mapper( cls, *arg, **kw ) + return mapper( class_, *args, **kwargs ) def assign_mapper( session, class_, *args, **kwargs ): - m = class_.mapper = session.mapper( class_, *args, **kwargs ) - for name in ( 'flush', ): - _monkeypatch_session_method( name, session, class_, make_list=True ) + m = class_.mapper = session_mapper( session, class_, *args, **kwargs ) return m diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/forms.py Tue Nov 03 12:52:00 2009 -0500 @@ -450,7 +450,7 @@ # create corresponding row in the form_definition_current table fd.form_definition_current = fdc fdc.latest_form = fd - trans.sa_session.save_or_update( fdc ) + trans.sa_session.add( fdc ) trans.sa_session.flush() msg = "The new form named '%s' has been created. " % (fd.name) return fd, msg diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 12:52:00 2009 -0500 @@ -726,7 +726,7 @@ share.history = history share.user = send_to_user session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() if history not in shared_histories: shared_histories.append( history ) diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/page.py Tue Nov 03 12:52:00 2009 -0500 @@ -135,7 +135,7 @@ page_revision.content = "" # Persist session = trans.sa_session - session.save_or_update( page ) + session.add( page ) session.flush() # Display the management page ## trans.set_message( "Page '%s' created" % page.title ) @@ -240,4 +240,4 @@ raise web.httpexceptions.HTTPNotFound() return trans.fill_template( "page/display.mako", page=page ) - \ No newline at end of file + diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Tue Nov 03 12:52:00 2009 -0500 @@ -30,7 +30,7 @@ user = trans.get_user() workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ @@ -53,13 +53,13 @@ user = trans.get_user() workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.c.deleted == False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .filter( model.StoredWorkflow.deleted == False ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() return trans.fill_template( "workflow/list_for_run.mako", workflows = workflows, @@ -91,7 +91,7 @@ share.stored_workflow = stored share.user = other session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() trans.set_message( "Workflow '%s' shared with user '%s'" % ( stored.name, other.email ) ) return trans.response.send_redirect( url_for( controller='workflow', action='sharing', id=id ) ) @@ -142,7 +142,7 @@ share.stored_workflow = stored share.user = trans.user session = trans.sa_session - session.save_or_update( share ) + session.add( share ) session.flush() # Redirect to load galaxy frames. return trans.response.send_redirect( url_for( controller='workflow' ) ) @@ -180,7 +180,7 @@ new_stored.user = user # Persist session = trans.sa_session - session.save_or_update( new_stored ) + session.add( new_stored ) session.flush() # Display the management page trans.set_message( 'Clone created with name "%s"' % new_stored.name ) @@ -205,7 +205,7 @@ stored_workflow.latest_workflow = workflow # Persist session = trans.sa_session - session.save_or_update( stored_workflow ) + session.add( stored_workflow ) session.flush() # Display the management page trans.set_message( "Workflow '%s' created" % stored_workflow.name ) @@ -514,7 +514,7 @@ stored.name = workflow_name workflow.stored_workflow = stored stored.latest_workflow = workflow - trans.sa_session.save_or_update( stored ) + trans.sa_session.add( stored ) trans.sa_session.flush() # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) @@ -656,12 +656,12 @@ ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] ) workflows = trans.sa_session.query( model.StoredWorkflow ) \ .filter_by( user=user, deleted=False ) \ - .order_by( desc( model.StoredWorkflow.c.update_time ) ) \ + .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \ .all() shared_by_others = trans.sa_session \ .query( model.StoredWorkflowUserShareAssociation ) \ .filter_by( user=user ) \ - .filter( model.StoredWorkflow.c.deleted == False ) \ + .filter( model.StoredWorkflow.deleted == False ) \ .all() return trans.fill_template( "workflow/configure_menu.mako", workflows=workflows, diff -r 80915982fdb2 -r 133252175425 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:52:00 2009 -0500 @@ -111,10 +111,10 @@ if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' - query = query.order_by( self.model_class.c.get( sort_key ).desc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).desc() ) else: sort_order = 'asc' - query = query.order_by( self.model_class.c.get( sort_key ).asc() ) + query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key # There might be a current row

1 0

[hg] galaxy 2946: Fix new functional tests script return code (f...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/80915982fdb2 changeset: 2946:80915982fdb2 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 11:28:34 2009 -0500 description: Fix new functional tests script return code (for buildbot) diffstat: scripts/functional_tests.py | 11 +++++++---- 1 files changed, 7 insertions(+), 4 deletions(-) diffs (34 lines): diff -r c96e886f883f -r 80915982fdb2 scripts/functional_tests.py --- a/scripts/functional_tests.py Tue Nov 03 10:26:42 2009 -0500 +++ b/scripts/functional_tests.py Tue Nov 03 11:28:34 2009 -0500 @@ -155,7 +155,7 @@ log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) - rval = False + success = False try: @@ -186,7 +186,7 @@ result = test_runner.run( tests ) - rval = result.wasSuccessful() + success = result.wasSuccessful() except: log.exception( "Failure running tests" ) @@ -206,7 +206,10 @@ app = None log.info( "Embedded Universe application stopped" ) - return rval + if success: + return 0 + else: + return 1 if __name__ == "__main__": - main() + sys.exit( main() )

1 0

[hg] galaxy 2947: Improved search functionality for history grid...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f776fa6045ba changeset: 2947:f776fa6045ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 12:58:13 2009 -0500 description: Improved search functionality for history grid: (a) generic free text search box and (b) advanced search using name, tag, deleted status, and shared status. diffstat: lib/galaxy/tags/tag_handler.py | 8 +- lib/galaxy/web/controllers/history.py | 145 +++++++++++++++++--- lib/galaxy/web/framework/helpers/grids.py | 1 + static/scripts/autocomplete_tagging.js | 2 +- templates/history/grid.mako | 250 +++++++++++++++++++--------------- test/base/twilltestcase.py | 18 +- test/functional/test_history_functions.py | 2 +- 7 files changed, 278 insertions(+), 148 deletions(-) diffs (649 lines): diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Nov 03 12:58:13 2009 -0500 @@ -3,6 +3,12 @@ class TagHandler( object ): + # Minimum tag length. + min_tag_len = 2 + + # Maximum tag length. + max_tag_len = 255 + # Tag separator. tag_separators = ',;' @@ -215,7 +221,7 @@ scrubbed_name = scrubbed_name[1:] # If name is too short or too long, return None. - if len(scrubbed_name) < 3 or len(scrubbed_name) > 255: + if len(scrubbed_name) < self.min_tag_len or len(scrubbed_name) > self.max_tag_len: return None return scrubbed_name diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 03 12:58:13 2009 -0500 @@ -5,6 +5,7 @@ from galaxy.model import History from galaxy.model.orm import * from galaxy.util.json import * +from galaxy.util.odict import odict from galaxy.tags.tag_handler import TagHandler from sqlalchemy.sql.expression import ClauseElement import webhelpers, logging, operator @@ -19,12 +20,29 @@ class HistoryListGrid( grids.Grid ): # Custom column types class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup ): + def __init( self, key, link, attach_popup, filterable ): grids.GridColumn.__init__(self, key, link, attach_popup) def get_value( self, trans, grid, history ): return history.get_display_name() + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by name. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -48,6 +66,7 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None + class TagsColumn( grids.GridColumn ): def __init__( self, col_name, key, filterable ): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -61,7 +80,7 @@ return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): - """ Modify query to include only histories with tags in column_filter. """ + """ Modify query to filter histories by tag. """ if column_filter == "All": pass elif column_filter: @@ -69,52 +88,115 @@ tag_handler = TagHandler() raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) for name, value in raw_tags.items(): - tag = tag_handler.get_tag_by_name( db_session, name ) - if tag: - query = query.filter( History.tags.any( tag_id=tag.id ) ) + if name: + # Search for tag names. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) if value: - query = query.filter( History.tags.any( value=value.lower() ) ) - else: - # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which - # will then yield a query that returns no results. - query = query.filter( History.tags.any( user_tname=name ) ) + # Search for tag values. + query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) return query def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - - + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "Active" : "False", "Deleted" : "True", "All": "All" } + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } accepted_filters = [] for label, val in accepted_filter_labels_and_vals.items(): args = { self.key: val } accepted_filters.append( grids.GridColumnFilter( label, args) ) return accepted_filters + + class SharingColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( History.users_shared_with == None ) + query = query.filter( History.importable == False ) + elif column_filter == "shared": + query = query.filter( History.users_shared_with != None ) + elif column_filter == "importable": + query = query.filter( History.importable == True ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["importable"] = "importable" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters + + class FreeTextSearchColumn( grids.GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to search tags and history names. """ + if column_filter == "All": + pass + elif column_filter: + # Build tags filter. + tag_handler = TagHandler() + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + tags_filter = None + for name, value in raw_tags.items(): + if name: + # Search for tag names. + tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) + if value: + # Search for tag values. + tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) + + # Build history name filter. + history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) + + # Apply filters to query. + if tags_filter: + query = query.filter( or_( tags_filter, history_name_filter ) ) + else: + query = query.filter( history_name_filter ) + return query + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = odict() + accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.iteritems(): + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters # Grid definition - title = "Stored histories" + title = "Saved Histories" model_class = model.History template='/history/grid.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), - attach_popup=True ), + attach_popup=True, filterable=True ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), TagsColumn( "Tags", key="tags", filterable=True), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Valid for filtering but invisible - DeletedColumn( "Status", key="deleted", visible=False, filterable=True ) + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable=True ), + SharingColumn( "Shared", key="shared", visible=False, filterable=True ), + FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. ] operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), @@ -131,7 +213,7 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] - default_filter = dict( deleted="False", tags="All" ) + default_filter = dict( name="All", deleted="False", tags="All", shared="All" ) num_rows_per_page = 50 preserve_state = False use_paging = True @@ -160,6 +242,7 @@ template='/history/grid.mako' model_class = model.History default_sort_key = "-update_time" + default_filter = {} columns = [ grids.GridColumn( "Name", key="name" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), @@ -374,6 +457,18 @@ trans.sa_session.flush() @web.expose + def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): + """Return autocomplete data for history names""" + user = trans.get_user() + if not user: + return + + ac_data = "" + for history in trans.sa_session.query( History ).filter_by( user=user ).filter( func.lower( History.name ) .like(q.lower() + "%") ): + ac_data = ac_data + history.name + "\n" + return ac_data + + @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): """Import another user's history via a shared URL""" msg = "" diff -r 80915982fdb2 -r f776fa6045ba lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 11:28:34 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 03 12:58:13 2009 -0500 @@ -183,6 +183,7 @@ query=query, cur_page_num = page_num, num_pages = num_pages, + default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, diff -r 80915982fdb2 -r f776fa6045ba static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Tue Nov 03 11:28:34 2009 -0500 +++ b/static/scripts/autocomplete_tagging.js Tue Nov 03 12:58:13 2009 -0500 @@ -309,7 +309,7 @@ new_value = new_value.replace(/^\s+|\s+$/g,""); // Too short? - if (new_value.length < 3) + if (new_value.length < 2) return false; // diff -r 80915982fdb2 -r f776fa6045ba templates/history/grid.mako --- a/templates/history/grid.mako Tue Nov 03 11:28:34 2009 -0500 +++ b/templates/history/grid.mako Tue Nov 03 12:58:13 2009 -0500 @@ -29,71 +29,20 @@ }); // Set up autocomplete for tag filter input. - var t = $("#input-tag-filter"); - t.keyup( function( e ) - { - if ( e.keyCode == 27 ) - { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode == 13 ) || // Return Key - ( e.keyCode == 188 ) || // Comma - ( e.keyCode == 32 ) // Space - ) - { - // - // Check input. - // - - new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete == true) - { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) != -1) - { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode == 188) || (e.keyCode == 32) ) - new_value = new_value.substring( 0 , new_value.length - 1 ); - - // Trim whitespace. - new_value = new_value.replace(/^\s+|\s+$/g,""); - - // Too short? - if (new_value.length < 3) - return false; - - // - // New tag OK. - // - } - }); + var t = $("#input-tags-filter"); - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) - { - tag_name_and_value = value.split(":"); - return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); - //var array = new Array(key, value, row_position, num_rows, - //search_term ); return "\"" + array.join("*") + "\""; - } var autocomplete_options = - { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - - $("#page-select").change(navigate_to_page); + // Set up autocomplete for name filter input. + var t2 = $("#input-name-filter"); + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -125,21 +74,52 @@ %endif %endif + // Filter and sort args for grid. + var filter_args = ${h.to_json_string(cur_filter_dict)}; + var sort_key = "${sort_key}"; + // - // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. + // Add tag to grid filter. // function add_tag_to_grid_filter(tag_name, tag_value) { - // Use tag as a filter: replace TAGNAME with tag_name and issue query. - <% - url_args = {} - if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": - url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" - else: - url_args["f-tags"] = "TAGNAME" - %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("TAGNAME", tag_name); + // Put tag name and value together. + var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); + add_condition_to_grid_filter("tags", tag, true); + } + + // + // Add a filter to the current grid filter; this adds the filter and then issues a request to refresh the grid. + // + function add_condition_to_grid_filter(name, value, append) + { + // Update filter arg with new condition. + if (append) + { + // Append value. + var cur_val = filter_args[name]; + if (cur_val != "All") + cur_val = cur_val + ", " + value; + else + cur_val = value; + filter_args[name] = cur_val; + } + else + { + // Replace value. + filter_args[name] = value; + } + + // Build URL with filter args, sort key. + var filter_arg_value_strs = new Array(); + var i = 0; + for (arg in filter_args) + { + filter_arg_value_strs[i++] = "f-" + arg + "=" + filter_args[arg]; + } + var filter_str = filter_arg_value_strs.join("&"); + var url_base = "${h.url_for( controller='history', action='list')}"; + var url = url_base + "?" + filter_str + "&sort=" + sort_key; self.location = url; } @@ -154,7 +134,7 @@ var url = url_base.replace("PAGE", page_num); self.location = url; } - + </script> </%def> @@ -175,47 +155,95 @@ <div class="grid-header"> <h2>${grid.title}</h2> - - ## Print grid filter. - <form name="history_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > - <strong>Filter:   </strong> - %for column in grid.columns: - %if column.filterable: - <span> by ${column.label.lower()}:</span> - ## For now, include special case to handle tags. - %if column.key == "tags": - %if cur_filter_dict[column.key] != "All": - <span class="filter" "style='font-style: italic'"> - ${cur_filter_dict[column.key]} - </span> - <span>|</span> + + ## Search box and more options filter at top of grid. + <div> + ## Grid search. TODO: use more elegant way to get free text search column. + <% column = grid.columns[-1] %> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if column.key in cur_filter_dict and cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" "style='font-style: italic'">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" + action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),false)" + method="get" > + ${column.label}: + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | %endif - <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> - <span>|</span> - %endif - - ## Handle other columns. - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - <span>     </span> + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> %endif %endfor - - ## Link to clear all filters. TODO: this should be the default filter or an empty filter. - <% - args = { "deleted" : "False", "tags" : "All" } - no_filter = GridColumnFilter("Clear Filter", args) - %> - <span><a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a></span> - </form> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + %if use_form: + </form> + %endif + </div> + + ## Advanced Search + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + ## Link to clear all filters. + <% + no_filter = GridColumnFilter("Clear All", default_filter_dict) + %> + <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + </td></tr> + %for column in grid.columns: + %if column.filterable: + <tr> + ## Show div if current filter has value that is different from the default filter. + %if cur_filter_dict[column.key] != default_filter_dict[column.key]: + <script type="text/javascript"> + $('#more-search-options').css("display", "block"); + </script> + %endif + <td style="padding-left: 10px">${column.label.lower()}:</td> + <td> + <% use_form = False %> + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" style="font-style: italic">${filter.label}</span> + %elif filter.label == "FREETEXT": + <form name="history_actions" action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),true)" + method="get" > + %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | + %endif + <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> + <% use_form = True %> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + %if use_form: + </form> + %endif + </td> + </tr> + %endif + %endfor + </table> + </div> </div> <form name="history_actions" action="${url()}" method="post" > <input type="hidden" name="page" value="${cur_page_num}"> @@ -291,7 +319,7 @@ extra = "" %> %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> %else: <td >${v}${extra}</td> %endif diff -r 80915982fdb2 -r f776fa6045ba test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Nov 03 11:28:34 2009 -0500 +++ b/test/base/twilltestcase.py Tue Nov 03 12:58:13 2009 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile, tempfile, re from itertools import * import twill @@ -311,20 +311,20 @@ def view_stored_active_histories( self, check_str='' ): self.home() self.visit_page( "history/list" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) + self.check_page_for_string( 'operation=Rename' ) + self.check_page_for_string( 'operation=Switch' ) + self.check_page_for_string( 'operation=Delete' ) if check_str: self.check_page_for_string( check_str ) self.home() def view_stored_deleted_histories( self, check_str='' ): self.home() self.visit_page( "history/list?f-deleted=True" ) - self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( 'Saved Histories' ) self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Undelete&id' ) + self.check_page_for_string( 'operation=Undelete' ) if check_str: self.check_page_for_string( check_str ) self.home() @@ -723,14 +723,14 @@ # Functions associated with browsers, cookies, HTML forms and page visits def check_page_for_string( self, patt ): - """Looks for 'patt' in the current browser page""" + """Looks for 'patt' in the current browser page""" page = self.last_page() for subpatt in patt.split(): if page.find( patt ) == -1: fname = self.write_temp_file( page ) errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) - + def write_temp_file( self, content ): fd, fname = tempfile.mkstemp( suffix='.html', prefix='twilltestcase-' ) f = os.fdopen( fd, "w" ) diff -r 80915982fdb2 -r f776fa6045ba test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Tue Nov 03 11:28:34 2009 -0500 +++ b/test/functional/test_history_functions.py Tue Nov 03 12:58:13 2009 -0500 @@ -179,7 +179,7 @@ self.share_current_history( regular_user1.email, check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing">shared' ) + self.view_stored_active_histories( check_str='operation=sharing' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare',

1 0

[hg] galaxy 2944: Changed the test user emails in the user_info ...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7594fc81bdfc changeset: 2944:7594fc81bdfc user: rc date: Tue Nov 03 07:58:24 2009 -0500 description: Changed the test user emails in the user_info functional tests diffstat: test/functional/test_user_info.py | 18 +++++++++--------- 1 files changed, 9 insertions(+), 9 deletions(-) diffs (60 lines): diff -r 6e657b4aa837 -r 7594fc81bdfc test/functional/test_user_info.py --- a/test/functional/test_user_info.py Mon Nov 02 16:52:32 2009 -0500 +++ b/test/functional/test_user_info.py Tue Nov 03 07:58:24 2009 -0500 @@ -75,7 +75,7 @@ # user a new user with 'Student' user info form form_one = get_latest_form(form_one_name) user_info_values=['Educational', 'Penn State'] - self.create_user_with_info( 'test1(a)bx.psu.edu', 'testuser', 'test1', + self.create_user_with_info( 'test11(a)bx.psu.edu', 'testuser', 'test11', user_info_forms='multiple', user_info_form_id=form_one.id, user_info_values=user_info_values ) @@ -98,7 +98,7 @@ # user a new user with 'Student' user info form form_one = get_latest_form(form_one_name) user_info_values=['Educational', 'Penn State'] - self.create_user_with_info( 'test2(a)bx.psu.edu', 'testuser', 'test2', + self.create_user_with_info( 'test12(a)bx.psu.edu', 'testuser', 'test12', user_info_forms='single', user_info_form_id=form_one.id, user_info_values=user_info_values ) @@ -110,31 +110,31 @@ def test_015_edit_user_info( self ): """Testing editing user info as a regular user""" self.logout() - self.login( 'test1(a)bx.psu.edu' ) + self.login( 'test11(a)bx.psu.edu' ) user = sa_session.query( galaxy.model.User ) \ - .filter( and_( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ) ).first() - self.edit_login_info( new_email='test1_new(a)bx.psu.edu', new_username='test1_new' ) + .filter( and_( galaxy.model.User.table.c.email=='test11(a)bx.psu.edu' ) ).first() + self.edit_login_info( new_email='test11_new(a)bx.psu.edu', new_username='test11_new' ) self.change_password('testuser', 'new_testuser') self.edit_user_info( ['Research', 'PSU'] ) def test_020_create_user_as_admin( self ): ''' Testing creating users as an admin ''' self.logout() - self.login( 'test2(a)bx.psu.edu' ) + self.login( 'test(a)bx.psu.edu' ) form_one = get_latest_form(form_one_name) user_info_values=['Educational', 'Penn State'] - self.create_user_with_info( 'test3(a)bx.psu.edu', 'testuser', 'test3', + self.create_user_with_info( 'test13(a)bx.psu.edu', 'testuser', 'test13', user_info_forms='single', user_info_form_id=form_one.id, user_info_values=user_info_values ) self.logout() self.login( 'test(a)bx.psu.edu' ) user = sa_session.query( galaxy.model.User ) \ - .filter( and_( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ) ).first() + .filter( and_( galaxy.model.User.table.c.email=='test13(a)bx.psu.edu' ) ).first() self.home() page = "admin/users?id=%s&operation=information&f-deleted=False" % self.security.encode_id( user.id ) self.visit_page( page ) self.check_page_for_string( 'Manage User Information' ) - self.check_page_for_string( 'test3(a)bx.psu.edu' ) + self.check_page_for_string( 'test13(a)bx.psu.edu' ) for value in user_info_values: self.check_page_for_string( value ) # lets delete the 'Student' user info form

1 0

[hg] galaxy 2945: Fixed a bug in the user selectbox in new reque...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c96e886f883f changeset: 2945:c96e886f883f user: rc date: Tue Nov 03 10:26:42 2009 -0500 description: Fixed a bug in the user selectbox in new requests page diffstat: lib/galaxy/web/controllers/requests_admin.py | 9 +++------ 1 files changed, 3 insertions(+), 6 deletions(-) diffs (34 lines): diff -r 7594fc81bdfc -r c96e886f883f lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Nov 03 07:58:24 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Nov 03 10:26:42 2009 -0500 @@ -377,8 +377,10 @@ msg=msg, messagetype=messagetype) def __select_user(self, trans, userid): + user_list = trans.sa_session.query( trans.app.model.User )\ + .order_by( trans.app.model.User.email.asc() ) user_ids = ['none'] - for user in trans.sa_session.query( trans.app.model.User ): + for user in user_list: if not user.deleted: user_ids.append(str(user.id)) select_user = SelectField('select_user', @@ -388,10 +390,6 @@ select_user.add_option('Select one', 'none', selected=True) else: select_user.add_option('Select one', 'none') - def __get_email(user): - return user.email - user_list = trans.sa_session.query( trans.app.model.User ) - #user_list.sort(key=__get_email) for user in user_list: if not user.deleted: if userid == str(user.id): @@ -399,7 +397,6 @@ else: select_user.add_option(user.email, user.id) return select_user - def __library_ui(self, trans, user, request=None, **kwd): ''' This method creates the data library & folder selectbox for new &

1 0

[hg] galaxy 2938: trackster: fix window resizing, wrong tiles be...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3aa07fc9512a changeset: 2938:3aa07fc9512a user: Kanwei Li <kanwei(a)gmail.com> date: Fri Oct 30 21:55:17 2009 -0400 description: trackster: fix window resizing, wrong tiles being displayed diffstat: static/scripts/trackster.js | 27 ++++++++++++++------------- 1 files changed, 14 insertions(+), 13 deletions(-) diffs (92 lines): diff -r dac542cca894 -r 3aa07fc9512a static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Oct 30 14:27:48 2009 -0400 +++ b/static/scripts/trackster.js Fri Oct 30 21:55:17 2009 -0400 @@ -7,7 +7,7 @@ DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", - CACHED_TILES = 5, + CACHED_TILES = 10, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), RIGHT_STRAND, LEFT_STRAND; @@ -22,7 +22,6 @@ left_img.onload = function() { LEFT_STRAND = CONTEXT.createPattern(left_img, "repeat"); } - var right_img_inv = new Image(); right_img_inv.src = "../images/visualization/strand_right_inv.png"; right_img_inv.onload = function() { @@ -182,10 +181,10 @@ var tile_index = Math.floor( low / resolution / DENSITY ); while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache - var key = this.view.zoom_level + "_" + tile_index; + var key = this.content_div.width() + '_' + this.view.zoom_level + '_' + tile_index; var cached = this.tile_cache.get(key); if ( cached ) { - // console.log("cached tile"); + // console.log("cached tile " + tile_index); var tile_low = tile_index * DENSITY * resolution; cached.css( { left: ( tile_low - this.view.low ) * w_scale @@ -194,9 +193,9 @@ parent_element.append( cached ); } else { tile_element = this.draw_tile( resolution, tile_index, parent_element, w_scale ); - } - if ( tile_element ) { - this.tile_cache.set(key, tile_element); + if ( tile_element ) { + this.tile_cache.set(key, tile_element); + } } tile_index += 1; } @@ -384,7 +383,7 @@ calc_slots: function( include_labels ) { // console.log("num vals: " + this.values.length); var end_ary = [], - scale = this.container_div.width() / (this.view.high - this.view.low), + scale = this.content_div.width() / (this.view.high - this.view.low), labels_scale = this.show_labels_scale, max_high = this.view.max_high, max_low = this.view.max_low; @@ -396,14 +395,15 @@ for (var i = 0, len = this.values.length; i < len; i++) { var f_start, f_end, feature = this.values[i]; if (include_labels) { - f_start = Math.floor( Math.max(max_low, (feature.start - max_low) * labels_scale) ); + f_start = Math.floor( (feature.start - max_low) * labels_scale ); f_start -= dummy_canvas.measureText(feature.name).width; - f_end = Math.ceil( Math.min(max_high, (feature.end - max_low) * labels_scale) ); + f_end = Math.ceil( (feature.end - max_low) * labels_scale ); } else { - f_start = Math.floor( Math.max(max_low, (feature.start - max_low) * scale) ); - f_end = Math.ceil( Math.min(max_high, (feature.end - max_low) * scale) ); + f_start = Math.floor( (feature.start - max_low) * scale ); + f_end = Math.ceil( (feature.end - max_low) * scale ); } // if (include_labels) { console.log(f_start, f_end); } + var j = 0; while (true) { if (end_ary[j] === undefined || end_ary[j] < f_start) { @@ -425,7 +425,7 @@ if (!this.values) { // Still loading return null; } - // console.log("drawing"); + // console.log("drawing " + tile_index); // Once we zoom in enough, show name labels if (w_scale > this.show_labels_scale && !this.showing_labels) { this.showing_labels = true; @@ -480,6 +480,7 @@ // Showing labels, blocks, details if (ctx.fillText) { ctx.fillText(feature.name, f_start - 1, y_center + 8); + // ctx.fillText(commatize(feature.start), f_start - 1, y_center + 8); } var blocks = feature.blocks; if (blocks) {

1 0

[hg] galaxy 2939: Bug fix for cleanup_datasets.py - use app.sa_s...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e8263ea83fa changeset: 2939:6e8263ea83fa user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Nov 02 09:54:18 2009 -0500 description: Bug fix for cleanup_datasets.py - use app.sa_session instead of self.sa_session. diffstat: scripts/cleanup_datasets/cleanup_datasets.py | 90 +++++++++++++++--------------- 1 files changed, 45 insertions(+), 45 deletions(-) diffs (156 lines): diff -r 3aa07fc9512a -r 6e8263ea83fa scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Fri Oct 30 21:55:17 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Mon Nov 02 09:54:18 2009 -0500 @@ -93,14 +93,14 @@ history_count = 0 start = time.time() if force_retry: - histories = self.sa_session.query( app.model.History ) \ - .filter( and_( app.model.History.table.c.user_id==None, - app.model.History.table.c.update_time < cutoff_time ) ) + histories = app.sa_session.query( app.model.History ) \ + .filter( and_( app.model.History.table.c.user_id==None, + app.model.History.table.c.update_time < cutoff_time ) ) else: - histories = self.sa_session.query( app.model.History ) \ - .filter( and_( app.model.History.table.c.user_id==None, - app.model.History.table.c.deleted==False, - app.model.History.table.c.update_time < cutoff_time ) ) + histories = app.sa_session.query( app.model.History ) \ + .filter( and_( app.model.History.table.c.user_id==None, + app.model.History.table.c.deleted==False, + app.model.History.table.c.update_time < cutoff_time ) ) for history in histories: if not info_only: print "Deleting history id ", history.id @@ -121,16 +121,16 @@ history_count = 0 start = time.time() if force_retry: - histories = self.sa_session.query( app.model.History ) \ - .filter( and_( app.model.History.table.c.deleted==True, - app.model.History.table.c.update_time < cutoff_time ) ) \ - .options( eagerload( 'datasets' ) ) + histories = app.sa_session.query( app.model.History ) \ + .filter( and_( app.model.History.table.c.deleted==True, + app.model.History.table.c.update_time < cutoff_time ) ) \ + .options( eagerload( 'datasets' ) ) else: - histories = self.sa_session.query( app.model.History ) \ - .filter( and_( app.model.History.table.c.deleted==True, - app.model.History.table.c.purged==False, - app.model.History.table.c.update_time < cutoff_time ) ) \ - .options( eagerload( 'datasets' ) ) + histories = app.sa_session.query( app.model.History ) \ + .filter( and_( app.model.History.table.c.deleted==True, + app.model.History.table.c.purged==False, + app.model.History.table.c.update_time < cutoff_time ) ) \ + .options( eagerload( 'datasets' ) ) for history in histories: for dataset_assoc in history.datasets: _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable @@ -158,14 +158,14 @@ library_count = 0 start = time.time() if force_retry: - libraries = self.sa_session.query( app.model.Library ) \ - .filter( and_( app.model.Library.table.c.deleted==True, - app.model.Library.table.c.update_time < cutoff_time ) ) + libraries = app.sa_session.query( app.model.Library ) \ + .filter( and_( app.model.Library.table.c.deleted==True, + app.model.Library.table.c.update_time < cutoff_time ) ) else: - libraries = self.sa_session.query( app.model.Library ) \ - .filter( and_( app.model.Library.table.c.deleted==True, - app.model.Library.table.c.purged==False, - app.model.Library.table.c.update_time < cutoff_time ) ) + libraries = app.sa_session.query( app.model.Library ) \ + .filter( and_( app.model.Library.table.c.deleted==True, + app.model.Library.table.c.purged==False, + app.model.Library.table.c.update_time < cutoff_time ) ) for library in libraries: _purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only ) if not info_only: @@ -187,14 +187,14 @@ folder_count = 0 start = time.time() if force_retry: - folders = self.sa_session.query( app.model.LibraryFolder ) \ - .filter( and_( app.model.LibraryFolder.table.c.deleted==True, - app.model.LibraryFolder.table.c.update_time < cutoff_time ) ) + folders = app.sa_session.query( app.model.LibraryFolder ) \ + .filter( and_( app.model.LibraryFolder.table.c.deleted==True, + app.model.LibraryFolder.table.c.update_time < cutoff_time ) ) else: - folders = self.sa_session.query( app.model.LibraryFolder ) \ - .filter( and_( app.model.LibraryFolder.table.c.deleted==True, - app.model.LibraryFolder.table.c.purged==False, - app.model.LibraryFolder.table.c.update_time < cutoff_time ) ) + folders = app.sa_session.query( app.model.LibraryFolder ) \ + .filter( and_( app.model.LibraryFolder.table.c.deleted==True, + app.model.LibraryFolder.table.c.purged==False, + app.model.LibraryFolder.table.c.update_time < cutoff_time ) ) for folder in folders: _purge_folder( folder, app, remove_from_disk, info_only = info_only ) folder_count += 1 @@ -241,7 +241,7 @@ deleted_instance_count = 0 for dataset_id in dataset_ids: print "######### Processing dataset id:", dataset_id - dataset = self.sa_session.query( app.model.Dataset ).get( dataset_id ) + dataset = app.sa_session.query( app.model.Dataset ).get( dataset_id ) if dataset.id not in skip and _dataset_is_deletable( dataset ): deleted_dataset_count += 1 for dataset_instance in dataset.history_associations + dataset.library_associations: @@ -261,16 +261,16 @@ disk_space = 0 start = time.time() if force_retry: - datasets = self.sa_session.query( app.model.Dataset ) \ - .filter( and_( app.model.Dataset.table.c.deleted==True, - app.model.Dataset.table.c.purgable==True, - app.model.Dataset.table.c.update_time < cutoff_time ) ) + datasets = app.sa_session.query( app.model.Dataset ) \ + .filter( and_( app.model.Dataset.table.c.deleted==True, + app.model.Dataset.table.c.purgable==True, + app.model.Dataset.table.c.update_time < cutoff_time ) ) else: - datasets = self.sa_session.query( app.model.Dataset ) \ - .filter( and_( app.model.Dataset.table.c.deleted==True, - app.model.Dataset.table.c.purgable==True, - app.model.Dataset.table.c.purged==False, - app.model.Dataset.table.c.update_time < cutoff_time ) ) + datasets = app.sa_session.query( app.model.Dataset ) \ + .filter( and_( app.model.Dataset.table.c.deleted==True, + app.model.Dataset.table.c.purgable==True, + app.model.Dataset.table.c.purged==False, + app.model.Dataset.table.c.update_time < cutoff_time ) ) for dataset in datasets: file_size = dataset.file_size _purge_dataset( dataset, remove_from_disk, info_only = info_only ) @@ -294,7 +294,7 @@ dataset_instance.mark_deleted( include_children = include_children ) dataset_instance.clear_associated_files() dataset_instance.flush() - self.sa_session.refresh( dataset_instance.dataset ) + app.sa_session.refresh( dataset_instance.dataset ) if is_deletable or _dataset_is_deletable( dataset_instance.dataset ): # Calling methods may have already checked _dataset_is_deletable, if so, is_deletable should be True _delete_dataset( dataset_instance.dataset, app, remove_from_disk, info_only=info_only, is_deletable=is_deletable ) @@ -317,12 +317,12 @@ metadata_files = [] #lets create a list of metadata files, then perform actions on them for hda in dataset.history_associations: - for metadata_file in self.sa_session.query( app.model.MetadataFile ) \ - .filter( app.model.MetadataFile.table.c.hda_id==hda.id ): + for metadata_file in app.sa_session.query( app.model.MetadataFile ) \ + .filter( app.model.MetadataFile.table.c.hda_id==hda.id ): metadata_files.append( metadata_file ) for lda in dataset.library_associations: - for metadata_file in self.sa_session.query( app.model.MetadataFile ) \ - .filter( app.model.MetadataFile.table.c.lda_id==lda.id ): + for metadata_file in app.sa_session.query( app.model.MetadataFile ) \ + .filter( app.model.MetadataFile.table.c.lda_id==lda.id ): metadata_files.append( metadata_file ) for metadata_file in metadata_files: print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id

1 0

[hg] galaxy 2940: User information forms first pass.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cd0596754ff1 changeset: 2940:cd0596754ff1 user: rc date: Mon Nov 02 13:30:17 2009 -0500 description: User information forms first pass. - added a foreign key in the galaxy_user table to the form_values table - separate user info page for viewing/editing user info - user addresses added to user info page diffstat: lib/galaxy/model/__init__.py | 18 +- lib/galaxy/model/mapping.py | 3 + lib/galaxy/model/migrate/versions/0025_user_info.py | 62 ++ lib/galaxy/web/controllers/admin.py | 42 +- lib/galaxy/web/controllers/library_common.py | 3 +- lib/galaxy/web/controllers/user.py | 604 ++++++++++++++++++++----- lib/galaxy/web/form_builder.py | 19 + lib/galaxy/web/framework/helpers/grids.py | 3 +- templates/admin/user/grid.mako | 2 +- templates/user/edit_address.mako | 33 + templates/user/index.mako | 5 +- templates/user/info.mako | 161 ++++++ templates/user/permissions.mako | 8 +- templates/user/register.mako | 87 +++ test/base/twilltestcase.py | 105 +++- test/functional/test_forms_and_requests.py | 39 +- test/functional/test_user_info.py | 149 ++++++ 17 files changed, 1134 insertions(+), 209 deletions(-) diffs (1702 lines): diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/model/__init__.py Mon Nov 02 13:30:17 2009 -0500 @@ -1098,7 +1098,8 @@ class FormDefinition( object ): types = Bunch( REQUEST = 'Sequencing Request Form', SAMPLE = 'Sequencing Sample Form', - LIBRARY_INFO_TEMPLATE = 'Library information template' ) + LIBRARY_INFO_TEMPLATE = 'Library information template', + USER_INFO = 'User Information' ) def __init__(self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None): self.name = name @@ -1203,21 +1204,6 @@ self.folder = folder self.state = state self.samples_list = [] - def add_sample(self, sample_name=None, sample_desc=None, sample_values=None): - # create a form_values row - values = trans.app.model.FormValues(self.type.sample_form, sample_values) - values.flush() - sample = Sample(sample_name, sample_desc, self, values) - sample.flush() - # set the initial state - state = self.type.states[0] - event = SampleEvent(sample, state) - event.flush() - # add this sample to the member array - self.samples_list.append(sample) - return sample - def delete_sample(self, sample_name): - pass def has_sample(self, sample_name): for s in self.samples: if s.name == sample_name: diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/model/mapping.py Mon Nov 02 13:30:17 2009 -0500 @@ -47,6 +47,7 @@ Column( "username", TrimmedString( 255 ), index=True, unique=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) @@ -781,6 +782,8 @@ _preferences=relation( UserPreference, backref="user", collection_class=attribute_mapped_collection('name')), # addresses=relation( UserAddress, # primaryjoin=( User.table.c.id == UserAddress.table.c.user_id ) ) + values=relation( FormValues, + primaryjoin=( User.table.c.form_values_id == FormValues.table.c.id ) ), ) ) # Set up proxy so that this syntax is possible: diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/model/migrate/versions/0025_user_info.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0025_user_info.py Mon Nov 02 13:30:17 2009 -0500 @@ -0,0 +1,62 @@ +""" +This script adds a foreign key to the form_values table in the galaxy_user table +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +from migrate.changeset import * +import datetime +now = datetime.datetime.utcnow +import sys, logging +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) + +def display_migration_details(): + print "========================================" + print "This script adds a foreign key to the form_values table in the galaxy_user table" + print "========================================" +def upgrade(): + display_migration_details() + # Load existing tables + metadata.reflect() + try: + User_table = Table( "galaxy_user", metadata, autoload=True ) + except NoSuchTableError: + User_table = None + log.debug( "Failed loading table galaxy_user" ) + if User_table: + try: + col = Column( "form_values_id", Integer, index=True ) + col.create( User_table ) + assert col is User_table.c.form_values_id + except Exception, e: + log.debug( "Adding column 'form_values_id' to galaxy_user table failed: %s" % ( str( e ) ) ) + try: + FormValues_table = Table( "form_values", metadata, autoload=True ) + except NoSuchTableError: + FormValues_table = None + log.debug( "Failed loading table form_values" ) + # Add 1 foreign key constraint to the form_values table + if User_table and FormValues_table: + try: + cons = ForeignKeyConstraint( [User_table.c.form_values_id], + [FormValues_table.c.id], + name='user_form_values_id_fk' ) + # Create the constraint + cons.create() + except Exception, e: + log.debug( "Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: %s" % ( str( e ) ) ) +def downgrade(): + pass \ No newline at end of file diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/web/controllers/admin.py Mon Nov 02 13:30:17 2009 -0500 @@ -41,7 +41,7 @@ model_class = model.User template='/admin/user/grid.mako' columns = [ - EmailColumn( "Email", link=( lambda item: dict( operation="user", id=item.id ) ), attach_popup=True ), + EmailColumn( "Email", link=( lambda item: dict( operation="information", id=item.id ) ), attach_popup=True ), UserNameColumn( "User Name", attach_popup=False ), GroupsColumn( "Groups", attach_popup=False ), RolesColumn( "Roles", attach_popup=False ), @@ -51,13 +51,15 @@ grids.GridColumn( "Deleted", key="deleted", visible=False ) ] operations = [ - grids.GridOperation( "reset_password", condition=( lambda item: not item.deleted ), allow_multiple=True ) + grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False ) + ] #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if # the setting is False - operations.append( grids.GridOperation( "delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "undelete", condition=( lambda item: item.deleted ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ) + operations.append( grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) ) + operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) + operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ) ) + operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ) standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -530,6 +532,9 @@ @web.expose @web.require_admin def create_new_user( self, trans, **kwargs ): + return trans.response.send_redirect( web.url_for( controller='user', + action='create', + admin_view='True' ) ) email = '' password = '' confirm = '' @@ -731,9 +736,9 @@ def users( self, trans, **kwargs ): if 'operation' in kwargs: operation = kwargs['operation'].lower() - if operation == "user": + if operation == "roles": return self.user( trans, **kwargs ) - if operation == "reset_password": + if operation == "reset password": return self.reset_user_password( trans, **kwargs ) if operation == "delete": return self.mark_user_deleted( trans, **kwargs ) @@ -743,10 +748,33 @@ return self.purge_user( trans, **kwargs ) if operation == "create": return self.create_new_user( trans, **kwargs ) + if operation == "information": + return self.user_info( trans, **kwargs ) # Render the list view return self.user_list_grid( trans, **kwargs ) @web.expose @web.require_admin + def user_info( self, trans, **kwd ): + ''' + This method displays the user information page which consists of login + information, public username, reset password & other user information + obtained during registration + ''' + print 'KWD', kwd + user_id = kwd.get( 'id', None ) + if not user_id: + message += "Invalid user id (%s) received" % str( user_id ) + trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message=util.sanitize_text( message ), + status='error' ) ) + user = get_user( trans, user_id ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True ) ) + @web.expose + @web.require_admin def user( self, trans, **kwd ): user_id = kwd.get( 'id', None ) message = '' diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Mon Nov 02 13:30:17 2009 -0500 @@ -242,7 +242,8 @@ trans.response.send_redirect( web.url_for( controller='forms', action='new', msg=msg, - messagetype='done' ) ) + messagetype='done', + form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) ) if params.get( 'add_info_template_button', False ): form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( kwd[ 'form_id' ] ) ) #fields = list( copy.deepcopy( form.fields ) ) diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Mon Nov 02 13:30:17 2009 -0500 @@ -6,6 +6,9 @@ from galaxy import util import logging, os, string, re from random import choice +from galaxy.web.controllers.forms import get_all_forms +from galaxy.web.form_builder import * +from galaxy.web.controllers import admin log = logging.getLogger( __name__ ) @@ -23,10 +26,11 @@ VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" ) class User( BaseController ): - edit_address_id = None + @web.expose def index( self, trans, **kwd ): return trans.fill_template( '/user/index.mako', user=trans.get_user() ) + @web.expose def change_password(self, trans, old_pass='', new_pass='', conf_pass='', **kwd): old_pass_err = new_pass_err = conf_pass_err = '' @@ -158,50 +162,392 @@ msg += ' <a href="%s">Click here</a> to return to the login page.' % web.url_for( controller='user', action='login' ) return trans.show_ok_message( msg, refresh_frames=refresh_frames ) @web.expose - def create( self, trans, email='', password='', confirm='', subscribe=False ): + def create( self, trans, **kwd ): + params = util.Params( kwd ) + email = util.restore_text( params.get('email', '') ) + username = util.restore_text( params.get('username', '') ) + password = util.restore_text( params.get('password', '') ) + confirm = util.restore_text( params.get('confirm', '') ) + subscribe = params.get('subscribe', False) + admin_view = params.get('admin_view', 'False') + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) if trans.app.config.require_login: refresh_frames = [ 'masthead', 'history', 'tools' ] else: refresh_frames = [ 'masthead', 'history' ] if not trans.app.config.allow_user_creation and not trans.user_is_admin(): return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) - email_error = password_error = confirm_error = None - if email: - if len( email ) == 0 or "@" not in email or "." not in email: - email_error = "Please enter a real email address" - elif len( email ) > 255: - email_error = "Email address exceeds maximum allowable length" - elif trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).all(): - email_error = "User with that email already exists" - elif len( password ) < 6: - password_error = "Please use a password of at least 6 characters" - elif password != confirm: - confirm_error = "Passwords do not match" - else: - user = trans.app.model.User( email=email ) - user.set_password_cleartext( password ) - user.flush() - trans.app.security_agent.create_private_user_role( user ) - # We set default user permissions, before we log in and set the default history permissions - trans.app.security_agent.user_set_default_permissions( user, default_access_private = trans.app.config.new_user_dataset_access_role_default_private ) + # + # Create the user, save all the user info and login to Galaxy + # + if params.get('create_user_button', None) == "Submit": + # check email and password validity + error = self.__validate(trans, params, email, password, confirm) + if error: + kwd[ 'msg' ] = error + kwd[ 'messagetype' ] = 'error' + kwd[ 'create_user_button' ] = None + return trans.response.send_redirect( web.url_for( controller='user', + action='create', + **kwd ) ) + # all the values are valid + user = trans.app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + user.flush() + trans.app.security_agent.create_private_user_role( user ) + # We set default user permissions, before we log in and set the default history permissions + trans.app.security_agent.user_set_default_permissions( user, default_access_private = trans.app.config.new_user_dataset_access_role_default_private ) + # save user info + self.__save_user_info(trans, user, action='create', new_user=True, **kwd) + if subscribe: + mail = os.popen("%s -t" % trans.app.config.sendmail_path, 'w') + mail.write("To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list." % (trans.app.config.mailing_join_addr,email) ) + if mail.close(): + return trans.show_warn_message( "Now logged in as " + user.email+". However, subscribing to the mailing list has failed.", refresh_frames=refresh_frames ) + if admin_view == 'False': # The handle_user_login() method has a call to the history_set_default_permissions() method # (needed when logging in with a history), user needs to have default permissions set before logging in trans.handle_user_login( user ) trans.log_event( "User created a new account" ) trans.log_event( "User logged in" ) - #subscribe user to email list - if subscribe: - mail = os.popen("%s -t" % trans.app.config.sendmail_path, 'w') - mail.write("To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list." % (trans.app.config.mailing_join_addr,email) ) - if mail.close(): - return trans.show_warn_message( "Now logged in as " + user.email+". However, subscribing to the mailing list has failed.", refresh_frames=refresh_frames ) + # subscribe user to email list return trans.show_ok_message( "Now logged in as " + user.email, refresh_frames=refresh_frames ) - return trans.show_form( - web.FormBuilder( web.url_for(), "Create account", submit_text="Create" ) - .add_text( "email", "Email address", value=email, error=email_error ) - .add_password( "password", "Password", value='', error=password_error ) - .add_password( "confirm", "Confirm password", value='', error=confirm_error ) - .add_input( "checkbox","Subscribe To Mailing List","subscribe", value='subscribe' ) ) + else: + trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Created new user account (%s)' % user.email, + status='done' ) ) + else: + # + # Show the user registration form + # + user_info_select, user_info_form, login_info, widgets = self.__user_info_ui(trans, **kwd) + return trans.fill_template( '/user/register.mako', + user_info_select=user_info_select, + user_info_form=user_info_form, widgets=widgets, + login_info=login_info, admin_view=admin_view, + msg=msg, messagetype=messagetype) + + def __save_user_info(self, trans, user, action, new_user=True, **kwd): + ''' + This method saves the user information for new users as well as editing user + info for existing users. For new users, the user info form is retrieved from + the one that user has selected. And for existing users, the user info form is + retrieved from the db. + ''' + params = util.Params( kwd ) + # get all the user information forms + user_info_forms = get_all_forms( trans, filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) + # if there are no user forms available then there is nothing to save + if not len( user_info_forms ): + return + if new_user: + user_info_type = params.get( 'user_info_select', 'none' ) + try: + user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(user_info_type)) + except: + return trans.response.send_redirect( web.url_for( controller='user', + action=action, + msg='Invalid user information form id', + messagetype='error') ) + else: + user_info_form = user.values.form_definition + values = [] + for index, field in enumerate(user_info_form.fields): + if field['type'] == 'AddressField': + value = util.restore_text(params.get('field_%i' % index, '')) + if value == 'new': + # save this new address in the list of this user's addresses + user_address = trans.app.model.UserAddress( user=user ) + user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, '')) + user_address.name = util.restore_text(params.get('field_%i_name' % index, '')) + user_address.institution = util.restore_text(params.get('field_%i_institution' % index, '')) + user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, '')) + user_address.city = util.restore_text(params.get('field_%i_city' % index, '')) + user_address.state = util.restore_text(params.get('field_%i_state' % index, '')) + user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, '')) + user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) + user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) + user_address.flush() + trans.user.refresh() + values.append(int(user_address.id)) + elif value == unicode('none'): + values.append('') + else: + values.append(int(value)) + else: + values.append(util.restore_text(params.get('field_%i' % index, ''))) + if new_user: + form_values = trans.app.model.FormValues(user_info_form, values) + form_values.flush() + user.values = form_values + else: # editing the user info of an existing user + user.values.content = values + user.values.flush() + user.flush() + def __validate_email(self, trans, params, email, user=None): + error = None + if user: + if user.email == email: + return None + if len(email) == 0 or "@" not in email or "." not in email: + error = "Please enter a real email address" + elif len(email) > 255: + error = "Email address exceeds maximum allowable length" + elif trans.sa_session.query( trans.app.model.User ).filter_by(email=email).all(): + error = "User with that email already exists" + return error + def __validate_password(self, trans, params, password, confirm): + error = None + if len(password) < 6: + error = "Please use a password of at least 6 characters" + elif password != confirm: + error = "Passwords do not match" + return error + + def __validate(self, trans, params, email, password, confirm): + error = self.__validate_email(trans, params, email) + if error: + return error + error = self.__validate_password(trans, params, password, confirm) + if error: + return error + if len(get_all_forms( trans, + filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.USER_INFO )): + if params.get('user_info_select', 'none') == 'none': + return 'Select the user type and the user information' + return None + + def __user_info_ui(self, trans, user=None, **kwd): + ''' + This method creates the user type select box & user information form widgets + and is called during user registration and editing user information. + If there exists only one user information form then show it after main + login info. However, if there are more than one user info forms then + show a selectbox containing all the forms, then the user can select + the one that fits the user's description the most + ''' + params = util.Params( kwd ) + # get all the user information forms + user_info_forms = get_all_forms( trans, filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) + user_info_select = None + if user: + if user.values: + selected_user_form_id = user.values.form_definition.id + else: + selected_user_form_id = 'none' + else: + selected_user_form_id = params.get( 'user_info_select', 'none' ) + # when there are more than one user information forms then show a select box + # list all these forms + if len(user_info_forms) > 1: + # create the select box + user_info_select = SelectField('user_info_select', refresh_on_change=True, + refresh_on_change_values=[str(u.id) for u in user_info_forms]) + if selected_user_form_id == 'none': + user_info_select.add_option('Select one', 'none', selected=True) + else: + user_info_select.add_option('Select one', 'none') + for u in user_info_forms: + if selected_user_form_id == str(u.id): + user_info_select.add_option(u.name, u.id, selected=True) + else: + user_info_select.add_option(u.name, u.id) + # when there is just one user information form the just render that form + elif len(user_info_forms) == 1: + selected_user_form_id = user_info_forms[0].id + # now, create the selected user form widgets starting with the basic + # login information + if user: + login_info = { 'Email': TextField( 'email', 40, user.email ), + 'Public Username': TextField( 'username', 40, user.username ), + 'Current Password': PasswordField( 'current', 40, '' ), + 'New Password': PasswordField( 'password', 40, '' ), + 'Confirm': PasswordField( 'confirm', 40, '' ) } + else: + login_info = { 'Email': TextField( 'email', 40, + util.restore_text( params.get('email', '') ) ), + 'Public Username': TextField( 'username', 40, + util.restore_text( params.get('username', '') ) ), + 'Password': PasswordField( 'password', 40, + util.restore_text( params.get('password', '') ) ), + 'Confirm': PasswordField( 'confirm', 40, + util.restore_text( params.get('confirm', '') ) ), + 'Subscribe To Mailing List': CheckboxField( 'subscribe', + util.restore_text( params.get('subscribe', '') ) ) } + # user information + try: + user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(selected_user_form_id)) + except: + return user_info_select, None, login_info, None + if user: + if user.values: + widgets = user_info_form.get_widgets(user=user, + contents=user.values.content, + **kwd) + else: + widgets = user_info_form.get_widgets(None, contents=[], **kwd) + else: + widgets = user_info_form.get_widgets(None, contents=[], **kwd) + return user_info_select, user_info_form, login_info, widgets + + @web.expose + def show_info( self, trans, **kwd ): + ''' + This method displays the user information page which consists of login + information, public username, reset password & other user information + obtained during registration + ''' + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + # check if this method is called from the admin perspective, + if params.get('admin_view', 'False') == 'True': + try: + user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'user_id', None ) ) ) + except: + return trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Invalid user', + status='error' ) ) + admin_view = True + else: + user = trans.user + admin_view = False + user_info_select, user_info_form, login_info, widgets = self.__user_info_ui(trans, user, **kwd) + # user's addresses + show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) + if show_filter == 'All': + addresses = [address for address in user.addresses] + elif show_filter == 'Deleted': + addresses = [address for address in user.addresses if address.deleted] + else: + addresses = [address for address in user.addresses if not address.deleted] + return trans.fill_template( '/user/info.mako', user=user, admin_view=admin_view, + user_info_select=user_info_select, + user_info_form=user_info_form, widgets=widgets, + login_info=login_info, + addresses=addresses, show_filter=show_filter, + msg=msg, messagetype=messagetype) + @web.expose + def edit_info( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get('admin_view', 'False') == 'True': + try: + user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'user_id', None ) ) ) + except: + return trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Invalid user', + status='error' ) ) + else: + user = trans.user + # + # Editing login info (email & username) + # + if params.get('login_info_button', None) == 'Save': + email = util.restore_text( params.get('email', '') ) + username = util.restore_text( params.get('username', '') ) + # validate the new values + error = self.__validate_email(trans, params, email, user) + if error: + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg=error, + messagetype='error') ) + # the new email & username + user.email = email + user.username = username + user.flush() + msg = 'The login information has been updated with the changes' + if params.get('admin_view', 'False') == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True, + msg=msg, + messagetype='done' ) ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg=msg, + messagetype='done') ) + # + # Change password + # + elif params.get('change_password_button', None) == 'Save': + password = util.restore_text( params.get('password', '') ) + confirm = util.restore_text( params.get('confirm', '') ) + # when from the user perspective, validate the current password + if params.get('admin_view', 'False') == 'False': + current = util.restore_text( params.get('current', '') ) + if not trans.user.check_password( current ): + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg='Invalid current password', + messagetype='error') ) + # validate the new values + error = self.__validate_password(trans, params, password, confirm) + if error: + if params.get('admin_view', 'False') == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True, + msg=error, + messagetype='error' ) ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg=error, + messagetype='error') ) + # save new password + user.set_password_cleartext( password ) + user.flush() + trans.log_event( "User change password" ) + msg = 'The password has been changed.' + if params.get('admin_view', 'False') == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True, + msg=msg, + messagetype='done' ) ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg=msg, + messagetype='done') ) + # + # Edit user information + # + elif params.get('edit_user_info_button', None) == 'Save': + self.__save_user_info(trans, user, "show_info", new_user=False, **kwd) + msg = "The user information has been updated with the changes." + if params.get('admin_view', 'False') == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True, + msg=msg, + messagetype='done' ) ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg=msg, + messagetype='done') ) + else: + if params.get('admin_view', 'False') == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True ) ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info' ) ) + @web.expose def reset_password( self, trans, email=None, **kwd ): error = '' @@ -305,7 +651,7 @@ country=country, phone=phone) user_address.flush() return trans.response.send_redirect( web.url_for( controller='user', - action='manage_addresses', + action='show_info', msg='Address <b>%s</b> has been added' % user_address.desc, messagetype='done') ) @@ -322,109 +668,123 @@ .add_text( "country", "Country", value=country, error=country_error ) .add_text( "phone", "Phone", value=phone, error=phone_error ) ) @web.expose - def edit_address( self, trans, address_id=None, short_desc='', name='', institution='', address1='', - address2='', city='', state='', postal_code='', country='', phone='' ): - import sys - - if trans.app.config.require_login: - refresh_frames = [ 'masthead', 'history', 'tools' ] + def edit_address( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + admin_view = params.get( 'admin_view', 'False' ) + error = '' + user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'user_id', None ) ) ) + try: + user_address = trans.sa_session.query( trans.app.model.UserAddress ).get(int(params.get( 'address_id', None ))) + except: + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=admin_view, + msg='Invalid address ID', + messagetype='error' ) ) + if params.get( 'edit_address_button', None ) == 'Save changes': + if not len( util.restore_text( params.get( 'short_desc', '' ) ) ): + error = 'Enter a short description for this address' + elif not len( util.restore_text( params.get( 'name', '' ) ) ): + error = 'Enter the full name' + elif not len( util.restore_text( params.get( 'institution', '' ) ) ): + error = 'Enter the institution associated with the user' + elif not len ( util.restore_text( params.get( 'address1', '' ) ) ): + error = 'Enter the address' + elif not len( util.restore_text( params.get( 'city', '' ) ) ): + error = 'Enter the city' + elif not len( util.restore_text( params.get( 'state', '' ) ) ): + error = 'Enter the state/province/region' + elif not len( util.restore_text( params.get( 'postal_code', '' ) ) ): + error = 'Enter the postal code' + elif not len( util.restore_text( params.get( 'country', '' ) ) ): + error = 'Enter the country' + else: + user_address.desc = util.restore_text( params.get( 'short_desc', '' ) ) + user_address.name = util.restore_text( params.get( 'name', '' ) ) + user_address.institution = util.restore_text( params.get( 'institution', '' ) ) + user_address.address = util.restore_text( params.get( 'address1', '' ) )+' '+util.restore_text( params.get( 'address2', '' ) ) + user_address.city = util.restore_text( params.get( 'city', '' ) ) + user_address.state = util.restore_text( params.get( 'state', '' ) ) + user_address.postal_code = util.restore_text( params.get( 'postal_code', '' ) ) + user_address.country = util.restore_text( params.get( 'country', '' ) ) + user_address.phone = util.restore_text( params.get( 'phone', '' ) ) + user_address.flush() + msg = 'Changes made to address <b>%s</b> are saved.' % user_address.desc + if admin_view == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user.id, + admin_view=True, + msg=msg, + messagetype='done' ) ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + msg=msg, + messagetype='done') ) else: - refresh_frames = [ 'masthead', 'history' ] - if not trans.app.config.allow_user_creation and not trans.user_is_admin(): - return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) - short_desc_error = name_error = institution_error = address1_error = city_error = None - address2_error = state_error = postal_code_error = country_error = phone_error = None - if short_desc: - if not len( short_desc ): - short_desc_error = 'Enter a short description for this address' - elif not len( name ): - name_error = 'Enter the full name' - elif not len( institution ): - institution_error = 'Enter the institution associated with the user' - elif not len ( address1 ): - address1_error = 'Enter the address' - elif not len( city ): - city_error = 'Enter the city' - elif not len( state ): - state_error = 'Enter the state/province/region' - elif not len( postal_code ): - postal_code_error = 'Enter the postal code' - elif not len( country ): - country_error = 'Enter the country' - else: - if self.edit_address_id: - try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( int( self.edit_address_id ) ) - except: - return trans.response.send_redirect( web.url_for( controller='user', - action='manage_addresses', - msg='Invalid address ID', - messagetype='error') ) - user_address.desc = short_desc - user_address.name = name - user_address.institution = institution - user_address.address = address1+' '+address2 - user_address.city = city - user_address.state = state - user_address.postal_code = postal_code - user_address.country = country - user_address.phone = phone - user_address.flush() - self.edit_address_id = None - return trans.response.send_redirect( web.url_for( controller='user', - action='manage_addresses', - msg='Changes made to address <b>%s</b> are saved.' % user_address.desc, - messagetype='done') ) - self.edit_address_id = address_id - return trans.show_form( - web.FormBuilder( web.url_for(), "Edit address", submit_text="Save changes" ) - .add_text( "short_desc", "Short address description", value=short_desc, error=short_desc_error ) - .add_text( "name", "Name", value=name, error=name_error ) - .add_text( "institution", "Institution", value=institution, error=institution_error ) - .add_text( "address1", "Address Line 1", value=address1, error=address1_error ) - .add_text( "address2", "Address Line 2", value=address2, error=address2_error ) - .add_text( "city", "City", value=city, error=city_error ) - .add_text( "state", "State/Province/Region", value=state, error=state_error ) - .add_text( "postal_code", "Postal Code", value=postal_code, error=postal_code_error ) - .add_text( "country", "Country", value=country, error=country_error ) - .add_text( "phone", "Phone", value=phone, error=phone_error ) ) + # show the address form with the current values filled in + # create the widgets for each address field + widgets = [] + widgets.append(dict(label='Short description', + widget=TextField( 'short_desc', 40, user_address.desc ) ) ) + widgets.append(dict(label='Name', + widget=TextField( 'name', 40, user_address.name ) ) ) + widgets.append(dict(label='Institution', + widget=TextField( 'institution', 40, user_address.institution ) ) ) + widgets.append(dict(label='Address Line 1', + widget=TextField( 'address1', 40, user_address.address ) ) ) + widgets.append(dict(label='City', + widget=TextField( 'city', 40, user_address.city ) ) ) + widgets.append(dict(label='State', + widget=TextField( 'state', 40, user_address.state ) ) ) + widgets.append(dict(label='Postal Code', + widget=TextField( 'postal_code', 40, user_address.postal_code ) ) ) + widgets.append(dict(label='Country', + widget=TextField( 'country', 40, user_address.country ) ) ) + widgets.append(dict(label='Phone', + widget=TextField( 'phone', 40, user_address.phone ) ) ) + return trans.fill_template( 'user/edit_address.mako', user=user, + address=user_address, admin_view=admin_view, + widgets=widgets, msg=msg, messagetype=messagetype) @web.expose - def delete_address( self, trans, address_id=None): - if trans.app.config.require_login: - refresh_frames = [ 'masthead', 'history', 'tools' ] - else: - refresh_frames = [ 'masthead', 'history' ] - if not trans.app.config.allow_user_creation and not trans.user_is_admin(): - return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) + def delete_address( self, trans, address_id=None, user_id=None, admin_view='False'): try: user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( int( address_id ) ) except: - return trans.fill_template( 'user/address.mako', - msg='Invalid address ID', - messagetype='error' ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user_id, + admin_view=admin_view, + msg='Invalid address ID', + messagetype='error' ) ) user_address.deleted = True user_address.flush() return trans.response.send_redirect( web.url_for( controller='user', - action='manage_addresses', + action='show_info', + admin_view=admin_view, + user_id=user_id, msg='Address <b>%s</b> deleted' % user_address.desc, messagetype='done') ) @web.expose - def undelete_address( self, trans, address_id=None): - if trans.app.config.require_login: - refresh_frames = [ 'masthead', 'history', 'tools' ] - else: - refresh_frames = [ 'masthead', 'history' ] - if not trans.app.config.allow_user_creation and not trans.user_is_admin(): - return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) + def undelete_address( self, trans, address_id=None, user_id=None, admin_view='False'): try: user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( int( address_id ) ) except: - return trans.fill_template( 'user/address.mako', - msg='Invalid address ID', - messagetype='error' ) + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + user_id=user_id, + admin_view=admin_view, + msg='Invalid address ID', + messagetype='error' ) ) user_address.deleted = False user_address.flush() return trans.response.send_redirect( web.url_for( controller='user', - action='manage_addresses', - msg='Address <b>%s</b> is restored' % user_address.desc, + action='show_info', + admin_view=admin_view, + user_id=user_id, + msg='Address <b>%s</b> undeleted' % user_address.desc, messagetype='done') ) + diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/web/form_builder.py Mon Nov 02 13:30:17 2009 -0500 @@ -33,6 +33,25 @@ def set_size(self, size): self.size = int( size ) +class PasswordField(BaseField): + """ + A password input box. text appears as "******" + + >>> print PasswordField( "foo" ).get_html() + <input type="password" name="foo" size="10" value=""> + >>> print PasswordField( "bins", size=4, value="default" ).get_html() + <input type="password" name="bins" size="4" value="default"> + """ + def __init__( self, name, size=None, value=None ): + self.name = name + self.size = int( size or 10 ) + self.value = value or "" + def get_html( self, prefix="" ): + return '<input type="password" name="%s%s" size="%d" value="%s">' \ + % ( prefix, self.name, self.size, escape(str(self.value), quote=True) ) + def set_size(self, size): + self.size = int( size ) + class NumberField(BaseField): """ A number input box. diff -r 6e8263ea83fa -r cd0596754ff1 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 02 09:54:18 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Nov 02 13:30:17 2009 -0500 @@ -266,10 +266,11 @@ return accepted_filters class GridOperation( object ): - def __init__( self, label, key=None, condition=None, allow_multiple=True, target=None, url_args=None ): + def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None ): self.label = label self.key = key self.allow_multiple = allow_multiple + self.allow_popup = allow_popup self.condition = condition self.target = target self.url_args = url_args diff -r 6e8263ea83fa -r cd0596754ff1 templates/admin/user/grid.mako --- a/templates/admin/user/grid.mako Mon Nov 02 09:54:18 2009 -0500 +++ b/templates/admin/user/grid.mako Mon Nov 02 13:30:17 2009 -0500 @@ -195,7 +195,7 @@ <td> <div popupmenu="grid-${i}-popup"> %for operation in grid.operations: - %if operation.allowed( item ): + %if operation.allowed( item ) and operation.allow_popup: <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> %endif %endfor diff -r 6e8263ea83fa -r cd0596754ff1 templates/user/edit_address.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/user/edit_address.mako Mon Nov 02 13:30:17 2009 -0500 @@ -0,0 +1,33 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif +</br> +</br> +<h3>Edit address</h3> + +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='show_info')}"> + <span>Manage User Information</span></a> + </li> +</ul> +<div class="toolForm"> +<form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_address', admin_view=admin_view, address_id=address.id, user_id=user.id )}" method="post" > + <div class="toolFormTitle">Edit address</div> + <div class="toolFormBody"> + %for field in widgets: + <div class="form-row"> + <label>${field[ 'label' ]}</label> + ${field[ 'widget' ].get_html()} + </div> + %endfor + <div class="form-row"> + <input type="submit" name="edit_address_button" value="Save changes"> + </div> + </div> +</form> +</div> \ No newline at end of file diff -r 6e8263ea83fa -r cd0596754ff1 templates/user/index.mako --- a/templates/user/index.mako Mon Nov 02 09:54:18 2009 -0500 +++ b/templates/user/index.mako Mon Nov 02 13:30:17 2009 -0500 @@ -7,11 +7,8 @@ %if user: <p>You are currently logged in as ${user.email}.</p> <ul> - <li><a href="${h.url_for( action='change_password' )}">${_('Change your password')}</a></li> - <li><a href="${h.url_for( action='change_email' )}">${_('Update your email address')}</a></li> - <li><a href="${h.url_for( action='change_username' )}">${_('Change your public username')}</a></li> + <li><a href="${h.url_for( action='show_info' )}">${_('Manage your information')}</a></li> <li><a href="${h.url_for( action='set_default_permissions' )}">${_('Change default permissions')}</a> for new histories</li> - <li><a href="${h.url_for( action='manage_addresses' )}">${_('Manage your addresses')}</a></li> <li><a href="${h.url_for( action='logout' )}">${_('Logout')}</a></li> </ul> %else: diff -r 6e8263ea83fa -r cd0596754ff1 templates/user/info.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/user/info.mako Mon Nov 02 13:30:17 2009 -0500 @@ -0,0 +1,161 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<h2>Manage User Information</h2> +%if not admin_view: + <ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='index')}"> + <span>User preferences</span></a> + </li> + </ul> +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#user_info" ).submit(); + } + }); +}); +</script> + +<div class="toolForm"> + <form name="login_info" id="login_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Login Information</div> + <div class="form-row"> + <label>Email</label> + ${login_info[ 'Email' ].get_html()} + </div> + <div class="form-row"> + <label>Public Username</label> + ${login_info[ 'Public Username' ].get_html()} + </div> + <div class="form-row"> + <input type="submit" name="login_info_button" value="Save"> + </div> + </form> + <form name="change_password" id="change_password" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Change Password</div> + %if not admin_view: + <div class="form-row"> + <label>Current Password</label> + ${login_info[ 'Current Password' ].get_html()} + </div> + %endif + <div class="form-row"> + <label>New Password</label> + ${login_info[ 'New Password' ].get_html()} + </div> + <div class="form-row"> + <label>Confirm</label> + ${login_info[ 'Confirm' ].get_html()} + </div> + <div class="form-row"> + <input type="submit" name="change_password_button" value="Save"> + </div> + </form> + %if user.values: + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">User information</div> + %if user_info_form: + %for field in widgets: + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + %if not user_info_select: + <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> + %endif + %endif + <div class="form-row"> + <input type="submit" name="edit_user_info_button" value="Save"> + </div> + </form> + %endif + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address' )}" method="post" > + <div class="toolFormTitle">User Addresses</div> + <div class="toolFormBody"> + %if user.addresses: + <div class="form-row"> + <div class="grid-header"> + ##<span class="title">Filter:</span> + %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): + %if i > 0: + <span>|</span> + %endif + %if show_filter == filter: + <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}"><b>${filter}</b></a></span> + %else: + <span class="filter"><a href="${h.url_for( controller='user', action='show_info', show_filter=filter, user_id=user.id, admin_view=admin_view )}">${filter}</a></span> + %endif + %endfor + </div> + </div> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}</label> + ${address.get_html()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', admin_view=admin_view, address_id=address.id, user_id=user.id )}"> + <span>Edit</span></a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"> + <span>Delete</span></a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', admin_view=admin_view, address_id=address.id, user_id=user.id)}"> + <span>Undelete</span></a> + %endif + + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + <div class="form-row"> + <input type="submit" value="Add a new address"> + </div> + </div> + </form> + + + + +</div> \ No newline at end of file diff -r 6e8263ea83fa -r cd0596754ff1 templates/user/permissions.mako --- a/templates/user/permissions.mako Mon Nov 02 09:54:18 2009 -0500 +++ b/templates/user/permissions.mako Mon Nov 02 13:30:17 2009 -0500 @@ -1,7 +1,13 @@ <%inherit file="/base.mako"/> <%def name="title()">Change Default Permissions on New Histories</%def> <%namespace file="/dataset/security_common.mako" import="render_permission_form" /> - +<br/><br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='index')}"> + <span>User preferences</span></a> + </li> +</ul> %if trans.user: ${render_permission_form( trans.user, trans.user.email, h.url_for(), trans.user.all_roles() )} %endif diff -r 6e8263ea83fa -r cd0596754ff1 templates/user/register.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/user/register.mako Mon Nov 02 13:30:17 2009 -0500 @@ -0,0 +1,87 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + + + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#registration" ).submit(); + } + }); +}); +</script> + +<div class="toolForm"> + <form name="registration" id="registration" action="${h.url_for( controller='user', action='create', admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">Create account</div> + <div class="form-row"> + <label>Email</label> + ${login_info[ 'Email' ].get_html()} + </div> + <div class="form-row"> + <label>Password</label> + ${login_info[ 'Password' ].get_html()} + </div> + <div class="form-row"> + <label>Confirm</label> + ${login_info[ 'Confirm' ].get_html()} + </div> + <div class="form-row"> + <label>Public Username</label> + ${login_info[ 'Public Username' ].get_html()} + <div class="toolParamHelp" style="clear: both;"> + Optional + </div> + </div> + <div class="form-row"> + <label>Subscribe To Mailing List</label> + ${login_info[ 'Subscribe To Mailing List' ].get_html()} + </div> + %if user_info_select: + <div class="form-row"> + <label>User type</label> + ${user_info_select.get_html()} + </div> + %endif + %if user_info_form: + %for field in widgets: + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + %if not user_info_select: + <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> + %endif + %endif + <div class="form-row"> + <input type="submit" name="create_user_button" value="Submit"> + </div> + </form> +</div> \ No newline at end of file diff -r 6e8263ea83fa -r cd0596754ff1 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Nov 02 09:54:18 2009 -0500 +++ b/test/base/twilltestcase.py Mon Nov 02 13:30:17 2009 -0500 @@ -596,13 +596,82 @@ # Functions associated with user accounts def create( self, email='test(a)bx.psu.edu', password='testuser' ): self.home() - self.visit_page( "user/create?email=%s&password=%s&confirm=%s" % ( email, password, password ) ) + self.visit_page( "user/create?email=%s&password=%s&confirm=%s&create_user_button=Submit" % ( email, password, password ) ) self.check_page_for_string( "Now logged in as %s" %email ) self.home() # Make sure a new private role was created for the user self.visit_page( "user/set_default_permissions" ) self.check_page_for_string( email ) self.home() + def create_user_with_info( self, email, password, username, user_info_forms, user_info_form_id, user_info_values ): + ''' + This method registers a new user and also provides use info + ''' + self.home() + if user_info_forms == 'multiple': + self.visit_page( "user/create?user_info_select=%i&admin_view=False" % user_info_form_id ) + else: + self.visit_page( "user/create?admin_view=False" ) + self.check_page_for_string( "Create account" ) + tc.fv( "1", "email", email ) + tc.fv( "1", "password", password ) + tc.fv( "1", "confirm", password ) + tc.fv( "1", "username", username ) + if user_info_forms == 'multiple': + self.check_page_for_string( "User type" ) + for index, info_value in enumerate(user_info_values): + tc.fv( "1", "field_%i" % index, info_value ) + tc.submit( "create_user_button" ) + self.check_page_for_string( "Now logged in as %s" % email ) + def create_user_with_info_as_admin( self, email, password, username, user_info_forms, user_info_form_id, user_info_values ): + ''' + This method registers a new user and also provides use info as an admin + ''' + self.home() + if user_info_forms == 'multiple': + self.visit_page( "admin/users?operation=create?user_info_select=%i&admin_view=False" % user_info_form_id ) + else: + self.visit_page( "admin/users?operation=create" ) + self.check_page_for_string( "Create account" ) + tc.fv( "1", "email", email ) + tc.fv( "1", "password", password ) + tc.fv( "1", "confirm", password ) + tc.fv( "1", "username", username ) + if user_info_forms == 'multiple': + self.check_page_for_string( "User type" ) + for index, info_value in enumerate(user_info_values): + tc.fv( "1", "field_%i" % index, info_value ) + tc.submit( "create_user_button" ) + self.check_page_for_string( "Created new user account (%s)" % email ) + def edit_login_info( self, new_email, new_username ): + self.home() + self.visit_page( "user/show_info" ) + self.check_page_for_string( "Manage User Information" ) + tc.fv( "1", "email", new_email ) + tc.fv( "1", "username", new_username ) + tc.submit( "login_info_button" ) + self.check_page_for_string( 'The login information has been updated with the changes' ) + self.check_page_for_string( new_email ) + self.check_page_for_string( new_username ) + def change_password( self, password, new_password ): + self.home() + self.visit_page( "user/show_info" ) + self.check_page_for_string( "Manage User Information" ) + tc.fv( "2", "current", password ) + tc.fv( "2", "password", new_password ) + tc.fv( "2", "confirm", new_password ) + tc.submit( "change_password_button" ) + self.check_page_for_string( 'The password has been changed.' ) + def edit_user_info( self, info_values ): + self.home() + self.visit_page( "user/show_info" ) + self.check_page_for_string( "Manage User Information" ) + for index, info_value in enumerate(info_values): + tc.fv( "3", "field_%i" % index, info_value ) + tc.submit( "edit_user_info_button" ) + self.check_page_for_string( "The user information has been updated with the changes." ) + for value in info_values: + self.check_page_for_string( value ) def user_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id=2 ): # role.id = 2 is Private Role for test2(a)bx.psu.edu # NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value # in each select list or twill throws an exception, which is: ParseError: OPTION outside of SELECT @@ -1161,19 +1230,8 @@ for index, field_value in enumerate(fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "create_request_button" ) - def create_request_admin( self, request_type_id, user_id, name, desc, library_id, fields ): - self.home() - self.visit_url( "%s/requests_admin/new?create=True&select_request_type=%i&library_id=%i" % ( self.url, - request_type_id, - library_id ) ) - self.check_page_for_string( 'Add a new request' ) - tc.fv( "1", "select_user", str(user_id) ) - tc.fv( "1", "name", name ) - tc.fv( "1", "desc", desc ) - tc.fv( "1", "library_id", str(library_id) ) - for index, field_value in enumerate(fields): - tc.fv( "1", "field_%i" % index, field_value ) - tc.submit( "create_request_button" ) + self.check_page_for_string( name ) + self.check_page_for_string( desc ) def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_folder_id, new_fields): self.home() self.visit_url( "%s/requests/edit?request_id=%i&show=True" % (self.url, request_id) ) @@ -1185,6 +1243,8 @@ for index, field_value in enumerate(new_fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "save_changes_request_button" ) + self.check_page_for_string( new_name ) + self.check_page_for_string( new_desc ) def add_samples( self, request_id, request_name, samples ): self.home() self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )) @@ -1196,6 +1256,11 @@ for field_index, field_value in enumerate(fields): tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) tc.submit( "save_samples_button" ) + for sample_name, fields in samples: + self.check_page_for_string( sample_name ) + self.check_page_for_string( 'Unsubmitted' ) + for field_value in fields: + self.check_page_for_string( field_value ) def submit_request( self, request_id, request_name ): self.home() self.visit_url( "%s/requests/submit_request?id=%i" % ( self.url, request_id )) @@ -1207,21 +1272,15 @@ for index, bar_code in enumerate(bar_codes): tc.fv( "1", "sample_%i_bar_code" % index, bar_code ) tc.submit( "save_bar_codes" ) - def change_sample_state( self, sample_name, sample_id, new_state_id, comment='' ): + self.check_page_for_string( 'Bar codes has been saved for this request' ) + def change_sample_state( self, sample_name, sample_id, new_state_id, new_state_name, comment='' ): self.home() self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) ) self.check_page_for_string( 'Events for Sample "%s"' % sample_name ) tc.fv( "1", "select_state", str(new_state_id) ) tc.fv( "1", "comment", comment ) tc.submit( "add_event_button" ) - # Address stuff - def create_address( self, address ): - self.home() - self.visit_url( "%s/user/new_address" % self.url ) - self.check_page_for_string( 'New address' ) - for name, value in address.iteritems(): - tc.fv( "1", name, value ) - tc.submit( "Save_button" ) + self.check_page_for_string( new_state_name ) # Library stuff def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" diff -r 6e8263ea83fa -r cd0596754ff1 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Mon Nov 02 09:54:18 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Mon Nov 02 13:30:17 2009 -0500 @@ -41,16 +41,11 @@ self.login( email='test(a)bx.psu.edu' ) # create a form global form_one_name - name = form_one_name desc = "This is Form One's description" formtype = galaxy.model.FormDefinition.types.REQUEST - self.create_form( name=name, desc=desc, formtype=formtype, num_fields=0 ) + self.create_form( name=form_one_name, desc=desc, formtype=formtype, num_fields=0 ) # Get the form_definition object for later tests - form_one = sa_session.query( galaxy.model.FormDefinition ) \ - .filter( and_( galaxy.model.FormDefinition.table.c.name==name, - galaxy.model.FormDefinition.table.c.desc==desc, - galaxy.model.FormDefinition.table.c.type==formtype ) ) \ - .all()[-1] + form_one = get_latest_form(form_one_name) assert form_one is not None, 'Problem retrieving form named "%s" from the database' % name # edit form & add few more fields new_name = "Request Form (Renamed)" @@ -83,20 +78,18 @@ def test_015_create_sample_form( self ): """Testing creating another form (for samples)""" global form_two_name - name = form_two_name desc = "This is Form One's description" formtype = 'Sequencing Sample Form' - self.create_form( name=name, desc=desc, formtype=formtype ) + self.create_form( name=form_two_name, desc=desc, formtype=formtype ) self.home() self.visit_page( 'forms/manage' ) - self.check_page_for_string( name ) + self.check_page_for_string( form_two_name ) self.check_page_for_string( desc ) self.check_page_for_string( formtype ) def test_020_create_request_type( self ): """Testing creating a new requestype""" request_form = get_latest_form(form_one_name) sample_form = get_latest_form(form_two_name) - print request_form.id, sample_form.id self.create_request_type(request_type_name, "test request type", str(request_form.id), str(sample_form.id), sample_states ) global request_type @@ -179,7 +172,6 @@ % ( self.url, address1[ 'short_desc' ], address1[ 'name' ], address1[ 'institution' ], address1[ 'address1' ], address1[ 'address2' ], address1[ 'city' ], address1[ 'state' ], address1[ 'postal_code' ], address1[ 'country' ], address1[ 'phone' ] ) - print url_str self.visit_url( url_str ) self.check_page_for_string( 'Address <b>%s</b> has been added' % address1[ 'short_desc' ] ) global regular_user @@ -201,8 +193,6 @@ # create the request request_name, request_desc = 'Request One', 'Request One Description' self.create_request(request_type.id, request_name, request_desc, library_one.id, 'none', fields) - self.check_page_for_string( request_name ) - self.check_page_for_string( request_desc ) global request_one request_one = sa_session.query( galaxy.model.Request ) \ .filter( and_( galaxy.model.Request.table.c.name==request_name, @@ -216,18 +206,11 @@ ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] # add samples to this request self.add_samples( request_one.id, request_one.name, samples ) - for sample_name, fields in samples: - self.check_page_for_string( sample_name ) - self.check_page_for_string( 'Unsubmitted' ) - for field_value in fields: - self.check_page_for_string( field_value ) # edit this request fields = ['option2', str(user_address.id), 'field three value (edited)'] self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) sa_session.refresh( request_one ) - self.check_page_for_string( request_name+' (Renamed)' ) - self.check_page_for_string( request_desc+' (Re-described)' ) # check if the request is showing in the 'unsubmitted' filter self.home() self.visit_url( '%s/requests/list?show_filter=Unsubmitted' % self.url ) @@ -256,15 +239,10 @@ # set bar codes for the samples bar_codes = [ '1234567890', '0987654321' ] self.add_bar_codes( request_one.id, request_one.name, bar_codes ) - self.check_page_for_string( 'Bar codes has been saved for this request' ) # change the states of all the samples of this request for sample in request_one.samples: - self.change_sample_state( sample.name, sample.id, request_type.states[1].id ) - self.check_page_for_string( request_type.states[1].name ) - self.check_page_for_string( request_type.states[1].desc ) - self.change_sample_state( sample.name, sample.id, request_type.states[2].id ) - self.check_page_for_string( request_type.states[2].name ) - self.check_page_for_string( request_type.states[2].desc ) + self.change_sample_state( sample.name, sample.id, request_type.states[1].id, request_type.states[1].name ) + self.change_sample_state( sample.name, sample.id, request_type.states[2].id, request_type.states[2].name ) self.home() sa_session.refresh( request_one ) # check if the request's state is now set to 'complete' @@ -300,11 +278,6 @@ ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] # add samples to this request self.add_samples( request_two.id, request_two.name, samples ) - for sample_name, fields in samples: - self.check_page_for_string( sample_name ) - self.check_page_for_string( 'Unsubmitted' ) - for field_value in fields: - self.check_page_for_string( field_value ) # submit the request self.submit_request( request_two.id, request_two.name ) sa_session.refresh( request_two ) diff -r 6e8263ea83fa -r cd0596754ff1 test/functional/test_user_info.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/functional/test_user_info.py Mon Nov 02 13:30:17 2009 -0500 @@ -0,0 +1,149 @@ +import galaxy.model +from galaxy.model.orm import * +from galaxy.model.mapping import context as sa_session +from base.twilltestcase import * + +not_logged_in_as_admin_security_msg = 'You must be logged in as an administrator to access this feature.' +logged_in_as_admin_security_msg = 'You must be an administrator to access this feature.' +not_logged_in_security_msg = 'You must be logged in to create/submit sequencing requests' +form_one_name = "Student" +form_two_name = "Researcher" + +def get_latest_form(form_name): + fdc_list = sa_session.query( galaxy.model.FormDefinitionCurrent ) \ + .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ + .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) + for fdc in fdc_list: + if form_name == fdc.latest_form.name: + return fdc.latest_form + return None + + +class TestUserInfo( TwillTestCase ): + def test_000_create_user_info_forms( self ): + """Testing creating a new user info form and editing it""" + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # create a the first form + global form_one_name + name = form_one_name + desc = "This is Student user info form's description" + formtype = galaxy.model.FormDefinition.types.USER_INFO + self.create_form( name=name, desc=desc, formtype=formtype, num_fields=0 ) + # Get the form_definition object for later tests + form_one = get_latest_form(form_one_name) + assert form_one is not None, 'Problem retrieving form named "%s" from the database' % name + # edit form & add few more fields + fields = [dict(name='Affiliation', + desc='The type of organization you are affiliated with', + type='SelectField', + required='optional', + selectlist=['Educational', 'Research', 'Commercial']), + dict(name='Name of Organization', + desc='', + type='TextField', + required='optional')] + form_one = get_latest_form(form_one_name) + self.form_add_field(form_one.id, form_one.name, form_one.desc, form_one.type, field_index=len(form_one.fields), fields=fields) + form_one_latest = get_latest_form(form_one_name) + assert len(form_one_latest.fields) == len(form_one.fields)+len(fields) + # create the second form + global form_two_name + name = form_two_name + desc = "This is Researcher user info form's description" + self.create_form( name=name, desc=desc, formtype=formtype, num_fields=0 ) + # Get the form_definition object for later tests + form_two = get_latest_form(form_two_name) + assert form_two is not None, 'Problem retrieving form named "%s" from the database' % name + # edit form & add few more fields + fields = [dict(name='Affiliation', + desc='The type of organization you are affiliated with', + type='SelectField', + required='optional', + selectlist=['Educational', 'Research', 'Commercial']), + dict(name='Name of Organization', + desc='', + type='TextField', + required='optional')] + form_two = get_latest_form(form_two_name) + self.form_add_field(form_two.id, form_two.name, form_two.desc, form_two.type, field_index=len(form_one.fields), fields=fields) + form_two_latest = get_latest_form(form_two_name) + assert len(form_two_latest.fields) == len(form_two.fields)+len(fields) + def test_005_user_reqistration_multiple_user_info_forms( self ): + ''' Testing user registration with multiple user info forms ''' + self.logout() + # user a new user with 'Student' user info form + form_one = get_latest_form(form_one_name) + user_info_values=['Educational', 'Penn State'] + self.create_user_with_info( 'test1(a)bx.psu.edu', 'testuser', 'test1', + user_info_forms='multiple', + user_info_form_id=form_one.id, + user_info_values=user_info_values ) + self.home() + self.visit_page( "user/show_info" ) + self.check_page_for_string( "Manage User Information" ) + for value in user_info_values: + self.check_page_for_string( value ) + def test_010_user_reqistration_single_user_info_forms( self ): + ''' Testing user registration with a single user info form ''' + # lets delete the 'Researcher' user info form + self.login( 'test(a)bx.psu.edu' ) + form_two_latest = get_latest_form(form_two_name) + form_two_latest.current.deleted = True + form_two_latest.current.flush() + self.home() + self.visit_page('forms/manage?show_filter=Deleted') + self.check_page_for_string(form_two_latest.name) + self.logout() + # user a new user with 'Student' user info form + form_one = get_latest_form(form_one_name) + user_info_values=['Educational', 'Penn State'] + self.create_user_with_info( 'test2(a)bx.psu.edu', 'testuser', 'test2', + user_info_forms='single', + user_info_form_id=form_one.id, + user_info_values=user_info_values ) + self.home() + self.visit_page( "user/show_info" ) + self.check_page_for_string( "Manage User Information" ) + for value in user_info_values: + self.check_page_for_string( value ) + def test_015_edit_user_info( self ): + """Testing editing user info as a regular user""" + self.logout() + self.login( 'test1(a)bx.psu.edu' ) + user = sa_session.query( galaxy.model.User ) \ + .filter( and_( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ) ).first() + self.edit_login_info( new_email='test1_new(a)bx.psu.edu', new_username='test1_new' ) + self.change_password('testuser', 'new_testuser') + self.edit_user_info( ['Research', 'PSU'] ) + def test_020_create_user_as_admin( self ): + ''' Testing creating users as an admin ''' + self.logout() + self.login( 'test2(a)bx.psu.edu' ) + form_one = get_latest_form(form_one_name) + user_info_values=['Educational', 'Penn State'] + self.create_user_with_info( 'test3(a)bx.psu.edu', 'testuser', 'test3', + user_info_forms='single', + user_info_form_id=form_one.id, + user_info_values=user_info_values ) + self.logout() + self.login( 'test(a)bx.psu.edu' ) + user = sa_session.query( galaxy.model.User ) \ + .filter( and_( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ) ).first() + self.home() + page = "admin/users?id=%s&operation=information&f-deleted=False" % self.security.encode_id( user.id ) + self.visit_page( page ) + self.check_page_for_string( 'Manage User Information' ) + self.check_page_for_string( 'test3(a)bx.psu.edu' ) + for value in user_info_values: + self.check_page_for_string( value ) + # lets delete the 'Student' user info form + self.login( 'test(a)bx.psu.edu' ) + form_one_latest = get_latest_form(form_one_name) + form_one_latest.current.deleted = True + form_one_latest.current.flush() + self.home() + self.visit_page('forms/manage?show_filter=Deleted') + self.check_page_for_string(form_one_latest.name) + self.logout() + \ No newline at end of file

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galaxy-dev November 2009